Last updated on 2020-09-25 07:49:51 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2 | 4.46 | 48.51 | 52.97 | WARN | |
| r-devel-linux-x86_64-debian-gcc | 1.2 | 3.75 | 37.35 | 41.10 | WARN | |
| r-devel-linux-x86_64-fedora-clang | 1.2 | 73.31 | WARN | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2 | 64.44 | WARN | |||
| r-devel-windows-ix86+x86_64 | 1.2 | 12.00 | 227.00 | 239.00 | OK | |
| r-patched-linux-x86_64 | 1.2 | 4.27 | 45.66 | 49.93 | WARN | |
| r-patched-solaris-x86 | 1.2 | 120.10 | WARN | |||
| r-release-linux-x86_64 | 1.2 | 4.78 | 45.32 | 50.10 | WARN | |
| r-release-macos-x86_64 | 1.2 | OK | ||||
| r-release-windows-ix86+x86_64 | 1.2 | 30.00 | 265.00 | 295.00 | OK | |
| r-oldrel-macos-x86_64 | 1.2 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.2 | 9.00 | 235.00 | 244.00 | OK |
Version: 1.2
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: 'lmms'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64
Version: 1.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'DynOmicsUserManual.Rmd' using knitr
Loading required package: ggplot2
dynOmics-package package:dynOmics R Documentation
_<08>F_<08>a_<08>s_<08>t _<08>F_<08>o_<08>u_<08>r_<08>i_<08>e_<08>r _<08>t_<08>r_<08>a_<08>n_<08>s_<08>f_<08>o_<08>r_<08>m _<08>t_<08>o _<08>e_<08>s_<08>t_<08>i_<08>m_<08>a_<08>t_<08>e _<08>d_<08>e_<08>l_<08>a_<08>y_<08>s _<08>i_<08>n _<08>e_<08>x_<08>p_<08>r_<08>e_<08>s_<08>s_<08>i_<08>o_<08>n _<08>i_<08>n_<08>i_<08>t_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n _<08>t_<08>o
_<08>i_<08>d_<08>e_<08>n_<08>t_<08>i_<08>f_<08>y _<08>a_<08>s_<08>s_<08>o_<08>c_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n_<08>s _<08>b_<08>e_<08>t_<08>w_<08>e_<08>e_<08>n _<08>t_<08>i_<08>m_<08>e _<08>c_<08>o_<08>u_<08>r_<08>s_<08>e '_<08>o_<08>m_<08>i_<08>c_<08>s' _<08>d_<08>a_<08>t_<08>a.
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
The package provides functions to identify associations within one
or between two time course 'omics' data and visualise the
associations : associateData to estimate the delays and identify
associations of data sets containing time course 'omics'
experiments; plot.associations: to visualise associated profiles.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
Package: dynOmics
Type: Package
Version: 1.2
Date: 2018-06-12
License: GPL-2
LazyLoad: yes
Functions for associating data: 'associateData'
Functions for summarization: 'summary.associations'
Functions for plots: 'plot.associations'
_<08>A_<08>u_<08>t_<08>h_<08>o_<08>r(_<08>s):
Jasmin Straube with contributions from Kim-Anh Le Cao, Emma Huang
and Anne Bernard
Maintainer: Jasmin Straube <j.straube@qimrberghofer.edu.au>
Metabolites package:dynOmics R Documentation
_<08>M_<08>e_<08>t_<08>a_<08>b_<08>o_<08>l_<08>i_<08>t_<08>e _<08>a_<08>n_<08>d _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Simulated data were received from Redestig et al., 2011.
Metabolite and transcript levels were obtained using an impulse
model (Chechik and Koller, 2009). Functions were used to model
five different metabolite patterns and for each metabolite 50
associated transcript levels. Time lags were introduced in the
range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
Simulated profiles have seven time points and normal distributed
noise was introduced with mean zero and standard deviation 0.1.
_<08>U_<08>s_<08>a_<08>g_<08>e:
data(Metabolites)
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
This data set contains the simulated expression of 5 metabolites
for 7 time points.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
* Metabolites. data matrix with 7 rows and 5 columns. Each row
represents an experimental time sample, and each column a
single metabolite.
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
The Metabolite Simulation Data is based on the the paper of
Redestig _et al._ (2011).
_<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
Redestig,H. and Costa,I.G. Detection and interpretation of
metabolite-transcript coresponses using combined profiling data.
_Bioinformatics_ *27*(13) (2011), pp. i357 65.
Transcripts package:dynOmics R Documentation
_<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Simulated data were received from Redestig et al., 2011.
Metabolite and transcript levels were obtained using an impulse
model (Chechik and Koller, 2009). Functions were used to model
five different metabolite patterns and for each metabolite 50
associated transcript levels. Time lags were introduced in the
range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
Simulated profiles have seven time points and normal distributed
noise was introduced with mean zero and standard deviation 0.1.
_<08>U_<08>s_<08>a_<08>g_<08>e:
data(Transcripts)
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
This data set contains the simulated expression 250 transcripts
for 7 time points.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
* Transcripts. data matrix with 7 rows and 250 columns. Each
row represents an experimental time sample, and each column a
single transcript.
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
The Transcript Simulation Data is based on the the paper of
Redestig _et al._ (2011).
_<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
Redestig,H. and Costa,I.G. Detection and interpretation of
metabolite-transcript coresponses using combined profiling data.
_Bioinformatics_ *27*(13) (2011), pp. i357 65.
Warning: Removed 126 row(s) containing missing values (geom_path).
Loading required package: lmms
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'lmms'
Installing package into '/tmp/Rtmp3vXXE8/RLIBS_6dd3140f6221'
(as 'lib' is unspecified)
Quitting from lines 168-177 (DynOmicsUserManual.Rmd)
Error: processing vignette 'DynOmicsUserManual.Rmd' failed with diagnostics:
trying to use CRAN without setting a mirror
--- failed re-building 'DynOmicsUserManual.Rmd'
SUMMARY: processing the following file failed:
'DynOmicsUserManual.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘DynOmicsUserManual.Rmd’ using knitr
Loading required package: ggplot2
dynOmics-package package:dynOmics R Documentation
_<08>F_<08>a_<08>s_<08>t _<08>F_<08>o_<08>u_<08>r_<08>i_<08>e_<08>r _<08>t_<08>r_<08>a_<08>n_<08>s_<08>f_<08>o_<08>r_<08>m _<08>t_<08>o _<08>e_<08>s_<08>t_<08>i_<08>m_<08>a_<08>t_<08>e _<08>d_<08>e_<08>l_<08>a_<08>y_<08>s _<08>i_<08>n _<08>e_<08>x_<08>p_<08>r_<08>e_<08>s_<08>s_<08>i_<08>o_<08>n _<08>i_<08>n_<08>i_<08>t_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n _<08>t_<08>o
_<08>i_<08>d_<08>e_<08>n_<08>t_<08>i_<08>f_<08>y _<08>a_<08>s_<08>s_<08>o_<08>c_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n_<08>s _<08>b_<08>e_<08>t_<08>w_<08>e_<08>e_<08>n _<08>t_<08>i_<08>m_<08>e _<08>c_<08>o_<08>u_<08>r_<08>s_<08>e '_<08>o_<08>m_<08>i_<08>c_<08>s' _<08>d_<08>a_<08>t_<08>a.
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
The package provides functions to identify associations within one
or between two time course 'omics' data and visualise the
associations : associateData to estimate the delays and identify
associations of data sets containing time course 'omics'
experiments; plot.associations: to visualise associated profiles.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
Package: dynOmics
Type: Package
Version: 1.2
Date: 2018-06-12
License: GPL-2
LazyLoad: yes
Functions for associating data: 'associateData'
Functions for summarization: 'summary.associations'
Functions for plots: 'plot.associations'
_<08>A_<08>u_<08>t_<08>h_<08>o_<08>r(_<08>s):
Jasmin Straube with contributions from Kim-Anh Le Cao, Emma Huang
and Anne Bernard
Maintainer: Jasmin Straube <j.straube@qimrberghofer.edu.au>
Metabolites package:dynOmics R Documentation
_<08>M_<08>e_<08>t_<08>a_<08>b_<08>o_<08>l_<08>i_<08>t_<08>e _<08>a_<08>n_<08>d _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Simulated data were received from Redestig et al., 2011.
Metabolite and transcript levels were obtained using an impulse
model (Chechik and Koller, 2009). Functions were used to model
five different metabolite patterns and for each metabolite 50
associated transcript levels. Time lags were introduced in the
range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
Simulated profiles have seven time points and normal distributed
noise was introduced with mean zero and standard deviation 0.1.
_<08>U_<08>s_<08>a_<08>g_<08>e:
data(Metabolites)
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
This data set contains the simulated expression of 5 metabolites
for 7 time points.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
• Metabolites. data matrix with 7 rows and 5 columns. Each row
represents an experimental time sample, and each column a
single metabolite.
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
The Metabolite Simulation Data is based on the the paper of
Redestig _et al._ (2011).
_<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
Redestig,H. and Costa,I.G. Detection and interpretation of
metabolite-transcript coresponses using combined profiling data.
_Bioinformatics_ *27*(13) (2011), pp. i357 65.
Transcripts package:dynOmics R Documentation
_<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Simulated data were received from Redestig et al., 2011.
Metabolite and transcript levels were obtained using an impulse
model (Chechik and Koller, 2009). Functions were used to model
five different metabolite patterns and for each metabolite 50
associated transcript levels. Time lags were introduced in the
range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
Simulated profiles have seven time points and normal distributed
noise was introduced with mean zero and standard deviation 0.1.
_<08>U_<08>s_<08>a_<08>g_<08>e:
data(Transcripts)
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
This data set contains the simulated expression 250 transcripts
for 7 time points.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
• Transcripts. data matrix with 7 rows and 250 columns. Each
row represents an experimental time sample, and each column a
single transcript.
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
The Transcript Simulation Data is based on the the paper of
Redestig _et al._ (2011).
_<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
Redestig,H. and Costa,I.G. Detection and interpretation of
metabolite-transcript coresponses using combined profiling data.
_Bioinformatics_ *27*(13) (2011), pp. i357 65.
Warning: Removed 126 row(s) containing missing values (geom_path).
Loading required package: lmms
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'lmms'
Installing package into '/home/hornik/tmp/scratch/RtmpXQ9Ack/RLIBS_721212724a4'
(as 'lib' is unspecified)
Quitting from lines 168-177 (DynOmicsUserManual.Rmd)
Error: processing vignette 'DynOmicsUserManual.Rmd' failed with diagnostics:
trying to use CRAN without setting a mirror
--- failed re-building ‘DynOmicsUserManual.Rmd’
SUMMARY: processing the following file failed:
‘DynOmicsUserManual.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘DynOmicsUserManual.Rmd’ using knitr
Loading required package: ggplot2
dynOmics-package package:dynOmics R Documentation
_<08>F_<08>a_<08>s_<08>t _<08>F_<08>o_<08>u_<08>r_<08>i_<08>e_<08>r _<08>t_<08>r_<08>a_<08>n_<08>s_<08>f_<08>o_<08>r_<08>m _<08>t_<08>o _<08>e_<08>s_<08>t_<08>i_<08>m_<08>a_<08>t_<08>e _<08>d_<08>e_<08>l_<08>a_<08>y_<08>s _<08>i_<08>n _<08>e_<08>x_<08>p_<08>r_<08>e_<08>s_<08>s_<08>i_<08>o_<08>n _<08>i_<08>n_<08>i_<08>t_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n _<08>t_<08>o
_<08>i_<08>d_<08>e_<08>n_<08>t_<08>i_<08>f_<08>y _<08>a_<08>s_<08>s_<08>o_<08>c_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n_<08>s _<08>b_<08>e_<08>t_<08>w_<08>e_<08>e_<08>n _<08>t_<08>i_<08>m_<08>e _<08>c_<08>o_<08>u_<08>r_<08>s_<08>e '_<08>o_<08>m_<08>i_<08>c_<08>s' _<08>d_<08>a_<08>t_<08>a.
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
The package provides functions to identify associations within one
or between two time course 'omics' data and visualise the
associations : associateData to estimate the delays and identify
associations of data sets containing time course 'omics'
experiments; plot.associations: to visualise associated profiles.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
Package: dynOmics
Type: Package
Version: 1.2
Date: 2018-06-12
License: GPL-2
LazyLoad: yes
Functions for associating data: 'associateData'
Functions for summarization: 'summary.associations'
Functions for plots: 'plot.associations'
_<08>A_<08>u_<08>t_<08>h_<08>o_<08>r(_<08>s):
Jasmin Straube with contributions from Kim-Anh Le Cao, Emma Huang
and Anne Bernard
Maintainer: Jasmin Straube <j.straube@qimrberghofer.edu.au>
Metabolites package:dynOmics R Documentation
_<08>M_<08>e_<08>t_<08>a_<08>b_<08>o_<08>l_<08>i_<08>t_<08>e _<08>a_<08>n_<08>d _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Simulated data were received from Redestig et al., 2011.
Metabolite and transcript levels were obtained using an impulse
model (Chechik and Koller, 2009). Functions were used to model
five different metabolite patterns and for each metabolite 50
associated transcript levels. Time lags were introduced in the
range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
Simulated profiles have seven time points and normal distributed
noise was introduced with mean zero and standard deviation 0.1.
_<08>U_<08>s_<08>a_<08>g_<08>e:
data(Metabolites)
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
This data set contains the simulated expression of 5 metabolites
for 7 time points.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
• Metabolites. data matrix with 7 rows and 5 columns. Each row
represents an experimental time sample, and each column a
single metabolite.
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
The Metabolite Simulation Data is based on the the paper of
Redestig _et al._ (2011).
_<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
Redestig,H. and Costa,I.G. Detection and interpretation of
metabolite-transcript coresponses using combined profiling data.
_Bioinformatics_ *27*(13) (2011), pp. i357 65.
Transcripts package:dynOmics R Documentation
_<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Simulated data were received from Redestig et al., 2011.
Metabolite and transcript levels were obtained using an impulse
model (Chechik and Koller, 2009). Functions were used to model
five different metabolite patterns and for each metabolite 50
associated transcript levels. Time lags were introduced in the
range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
Simulated profiles have seven time points and normal distributed
noise was introduced with mean zero and standard deviation 0.1.
_<08>U_<08>s_<08>a_<08>g_<08>e:
data(Transcripts)
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
This data set contains the simulated expression 250 transcripts
for 7 time points.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
• Transcripts. data matrix with 7 rows and 250 columns. Each
row represents an experimental time sample, and each column a
single transcript.
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
The Transcript Simulation Data is based on the the paper of
Redestig _et al._ (2011).
_<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
Redestig,H. and Costa,I.G. Detection and interpretation of
metabolite-transcript coresponses using combined profiling data.
_Bioinformatics_ *27*(13) (2011), pp. i357 65.
Warning: Removed 126 row(s) containing missing values (geom_path).
Loading required package: lmms
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'lmms'
Installing package into '/tmp/Rtmp3LTKdc/RLIBS_37224f736042ac'
(as 'lib' is unspecified)
Quitting from lines 168-177 (DynOmicsUserManual.Rmd)
Error: processing vignette 'DynOmicsUserManual.Rmd' failed with diagnostics:
trying to use CRAN without setting a mirror
--- failed re-building ‘DynOmicsUserManual.Rmd’
SUMMARY: processing the following file failed:
‘DynOmicsUserManual.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘DynOmicsUserManual.Rmd’ using knitr
Loading required package: ggplot2
dynOmics-package package:dynOmics R Documentation
_<08>F_<08>a_<08>s_<08>t _<08>F_<08>o_<08>u_<08>r_<08>i_<08>e_<08>r _<08>t_<08>r_<08>a_<08>n_<08>s_<08>f_<08>o_<08>r_<08>m _<08>t_<08>o _<08>e_<08>s_<08>t_<08>i_<08>m_<08>a_<08>t_<08>e _<08>d_<08>e_<08>l_<08>a_<08>y_<08>s _<08>i_<08>n _<08>e_<08>x_<08>p_<08>r_<08>e_<08>s_<08>s_<08>i_<08>o_<08>n _<08>i_<08>n_<08>i_<08>t_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n _<08>t_<08>o
_<08>i_<08>d_<08>e_<08>n_<08>t_<08>i_<08>f_<08>y _<08>a_<08>s_<08>s_<08>o_<08>c_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n_<08>s _<08>b_<08>e_<08>t_<08>w_<08>e_<08>e_<08>n _<08>t_<08>i_<08>m_<08>e _<08>c_<08>o_<08>u_<08>r_<08>s_<08>e '_<08>o_<08>m_<08>i_<08>c_<08>s' _<08>d_<08>a_<08>t_<08>a.
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
The package provides functions to identify associations within one
or between two time course 'omics' data and visualise the
associations : associateData to estimate the delays and identify
associations of data sets containing time course 'omics'
experiments; plot.associations: to visualise associated profiles.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
Package: dynOmics
Type: Package
Version: 1.2
Date: 2018-06-12
License: GPL-2
LazyLoad: yes
Functions for associating data: 'associateData'
Functions for summarization: 'summary.associations'
Functions for plots: 'plot.associations'
_<08>A_<08>u_<08>t_<08>h_<08>o_<08>r(_<08>s):
Jasmin Straube with contributions from Kim-Anh Le Cao, Emma Huang
and Anne Bernard
Maintainer: Jasmin Straube <j.straube@qimrberghofer.edu.au>
Metabolites package:dynOmics R Documentation
_<08>M_<08>e_<08>t_<08>a_<08>b_<08>o_<08>l_<08>i_<08>t_<08>e _<08>a_<08>n_<08>d _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Simulated data were received from Redestig et al., 2011.
Metabolite and transcript levels were obtained using an impulse
model (Chechik and Koller, 2009). Functions were used to model
five different metabolite patterns and for each metabolite 50
associated transcript levels. Time lags were introduced in the
range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
Simulated profiles have seven time points and normal distributed
noise was introduced with mean zero and standard deviation 0.1.
_<08>U_<08>s_<08>a_<08>g_<08>e:
data(Metabolites)
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
This data set contains the simulated expression of 5 metabolites
for 7 time points.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
• Metabolites. data matrix with 7 rows and 5 columns. Each row
represents an experimental time sample, and each column a
single metabolite.
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
The Metabolite Simulation Data is based on the the paper of
Redestig _et al._ (2011).
_<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
Redestig,H. and Costa,I.G. Detection and interpretation of
metabolite-transcript coresponses using combined profiling data.
_Bioinformatics_ *27*(13) (2011), pp. i357 65.
Transcripts package:dynOmics R Documentation
_<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Simulated data were received from Redestig et al., 2011.
Metabolite and transcript levels were obtained using an impulse
model (Chechik and Koller, 2009). Functions were used to model
five different metabolite patterns and for each metabolite 50
associated transcript levels. Time lags were introduced in the
range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
Simulated profiles have seven time points and normal distributed
noise was introduced with mean zero and standard deviation 0.1.
_<08>U_<08>s_<08>a_<08>g_<08>e:
data(Transcripts)
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
This data set contains the simulated expression 250 transcripts
for 7 time points.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
• Transcripts. data matrix with 7 rows and 250 columns. Each
row represents an experimental time sample, and each column a
single transcript.
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
The Transcript Simulation Data is based on the the paper of
Redestig _et al._ (2011).
_<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
Redestig,H. and Costa,I.G. Detection and interpretation of
metabolite-transcript coresponses using combined profiling data.
_Bioinformatics_ *27*(13) (2011), pp. i357 65.
Warning: Removed 126 row(s) containing missing values (geom_path).
Loading required package: lmms
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'lmms'
Installing package into '/data/gannet/ripley/R/packages/tests-devel/dynOmics.Rcheck'
(as 'lib' is unspecified)
Quitting from lines 168-177 (DynOmicsUserManual.Rmd)
Error: processing vignette 'DynOmicsUserManual.Rmd' failed with diagnostics:
trying to use CRAN without setting a mirror
--- failed re-building ‘DynOmicsUserManual.Rmd’
SUMMARY: processing the following file failed:
‘DynOmicsUserManual.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘DynOmicsUserManual.Rmd’ using knitr
Loading required package: ggplot2
dynOmics-package package:dynOmics R Documentation
_<08>F_<08>a_<08>s_<08>t _<08>F_<08>o_<08>u_<08>r_<08>i_<08>e_<08>r _<08>t_<08>r_<08>a_<08>n_<08>s_<08>f_<08>o_<08>r_<08>m _<08>t_<08>o _<08>e_<08>s_<08>t_<08>i_<08>m_<08>a_<08>t_<08>e _<08>d_<08>e_<08>l_<08>a_<08>y_<08>s _<08>i_<08>n _<08>e_<08>x_<08>p_<08>r_<08>e_<08>s_<08>s_<08>i_<08>o_<08>n _<08>i_<08>n_<08>i_<08>t_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n _<08>t_<08>o
_<08>i_<08>d_<08>e_<08>n_<08>t_<08>i_<08>f_<08>y _<08>a_<08>s_<08>s_<08>o_<08>c_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n_<08>s _<08>b_<08>e_<08>t_<08>w_<08>e_<08>e_<08>n _<08>t_<08>i_<08>m_<08>e _<08>c_<08>o_<08>u_<08>r_<08>s_<08>e '_<08>o_<08>m_<08>i_<08>c_<08>s' _<08>d_<08>a_<08>t_<08>a.
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
The package provides functions to identify associations within one
or between two time course 'omics' data and visualise the
associations : associateData to estimate the delays and identify
associations of data sets containing time course 'omics'
experiments; plot.associations: to visualise associated profiles.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
Package: dynOmics
Type: Package
Version: 1.2
Date: 2018-06-12
License: GPL-2
LazyLoad: yes
Functions for associating data: 'associateData'
Functions for summarization: 'summary.associations'
Functions for plots: 'plot.associations'
_<08>A_<08>u_<08>t_<08>h_<08>o_<08>r(_<08>s):
Jasmin Straube with contributions from Kim-Anh Le Cao, Emma Huang
and Anne Bernard
Maintainer: Jasmin Straube <j.straube@qimrberghofer.edu.au>
Metabolites package:dynOmics R Documentation
_<08>M_<08>e_<08>t_<08>a_<08>b_<08>o_<08>l_<08>i_<08>t_<08>e _<08>a_<08>n_<08>d _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Simulated data were received from Redestig et al., 2011.
Metabolite and transcript levels were obtained using an impulse
model (Chechik and Koller, 2009). Functions were used to model
five different metabolite patterns and for each metabolite 50
associated transcript levels. Time lags were introduced in the
range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
Simulated profiles have seven time points and normal distributed
noise was introduced with mean zero and standard deviation 0.1.
_<08>U_<08>s_<08>a_<08>g_<08>e:
data(Metabolites)
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
This data set contains the simulated expression of 5 metabolites
for 7 time points.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
• Metabolites. data matrix with 7 rows and 5 columns. Each row
represents an experimental time sample, and each column a
single metabolite.
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
The Metabolite Simulation Data is based on the the paper of
Redestig _et al._ (2011).
_<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
Redestig,H. and Costa,I.G. Detection and interpretation of
metabolite-transcript coresponses using combined profiling data.
_Bioinformatics_ *27*(13) (2011), pp. i357 65.
Transcripts package:dynOmics R Documentation
_<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Simulated data were received from Redestig et al., 2011.
Metabolite and transcript levels were obtained using an impulse
model (Chechik and Koller, 2009). Functions were used to model
five different metabolite patterns and for each metabolite 50
associated transcript levels. Time lags were introduced in the
range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
Simulated profiles have seven time points and normal distributed
noise was introduced with mean zero and standard deviation 0.1.
_<08>U_<08>s_<08>a_<08>g_<08>e:
data(Transcripts)
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
This data set contains the simulated expression 250 transcripts
for 7 time points.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
• Transcripts. data matrix with 7 rows and 250 columns. Each
row represents an experimental time sample, and each column a
single transcript.
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
The Transcript Simulation Data is based on the the paper of
Redestig _et al._ (2011).
_<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
Redestig,H. and Costa,I.G. Detection and interpretation of
metabolite-transcript coresponses using combined profiling data.
_Bioinformatics_ *27*(13) (2011), pp. i357 65.
Warning: Removed 126 row(s) containing missing values (geom_path).
Loading required package: lmms
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'lmms'
Installing package into '/tmp/RtmpWUpeLR/RLIBS_2d3d61b797ab'
(as 'lib' is unspecified)
Quitting from lines 168-177 (DynOmicsUserManual.Rmd)
Error: processing vignette 'DynOmicsUserManual.Rmd' failed with diagnostics:
trying to use CRAN without setting a mirror
--- failed re-building ‘DynOmicsUserManual.Rmd’
SUMMARY: processing the following file failed:
‘DynOmicsUserManual.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘DynOmicsUserManual.Rmd’ using knitr
Loading required package: ggplot2
dynOmics-package package:dynOmics R Documentation
_<08>F_<08>a_<08>s_<08>t _<08>F_<08>o_<08>u_<08>r_<08>i_<08>e_<08>r _<08>t_<08>r_<08>a_<08>n_<08>s_<08>f_<08>o_<08>r_<08>m _<08>t_<08>o _<08>e_<08>s_<08>t_<08>i_<08>m_<08>a_<08>t_<08>e _<08>d_<08>e_<08>l_<08>a_<08>y_<08>s _<08>i_<08>n _<08>e_<08>x_<08>p_<08>r_<08>e_<08>s_<08>s_<08>i_<08>o_<08>n _<08>i_<08>n_<08>i_<08>t_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n _<08>t_<08>o
_<08>i_<08>d_<08>e_<08>n_<08>t_<08>i_<08>f_<08>y _<08>a_<08>s_<08>s_<08>o_<08>c_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n_<08>s _<08>b_<08>e_<08>t_<08>w_<08>e_<08>e_<08>n _<08>t_<08>i_<08>m_<08>e _<08>c_<08>o_<08>u_<08>r_<08>s_<08>e '_<08>o_<08>m_<08>i_<08>c_<08>s' _<08>d_<08>a_<08>t_<08>a.
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
The package provides functions to identify associations within one
or between two time course 'omics' data and visualise the
associations : associateData to estimate the delays and identify
associations of data sets containing time course 'omics'
experiments; plot.associations: to visualise associated profiles.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
Package: dynOmics
Type: Package
Version: 1.2
Date: 2018-06-12
License: GPL-2
LazyLoad: yes
Functions for associating data: 'associateData'
Functions for summarization: 'summary.associations'
Functions for plots: 'plot.associations'
_<08>A_<08>u_<08>t_<08>h_<08>o_<08>r(_<08>s):
Jasmin Straube with contributions from Kim-Anh Le Cao, Emma Huang
and Anne Bernard
Maintainer: Jasmin Straube <j.straube@qimrberghofer.edu.au>
Metabolites package:dynOmics R Documentation
_<08>M_<08>e_<08>t_<08>a_<08>b_<08>o_<08>l_<08>i_<08>t_<08>e _<08>a_<08>n_<08>d _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Simulated data were received from Redestig et al., 2011.
Metabolite and transcript levels were obtained using an impulse
model (Chechik and Koller, 2009). Functions were used to model
five different metabolite patterns and for each metabolite 50
associated transcript levels. Time lags were introduced in the
range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
Simulated profiles have seven time points and normal distributed
noise was introduced with mean zero and standard deviation 0.1.
_<08>U_<08>s_<08>a_<08>g_<08>e:
data(Metabolites)
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
This data set contains the simulated expression of 5 metabolites
for 7 time points.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
• Metabolites. data matrix with 7 rows and 5 columns. Each row
represents an experimental time sample, and each column a
single metabolite.
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
The Metabolite Simulation Data is based on the the paper of
Redestig _et al._ (2011).
_<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
Redestig,H. and Costa,I.G. Detection and interpretation of
metabolite-transcript coresponses using combined profiling data.
_Bioinformatics_ *27*(13) (2011), pp. i357 65.
Transcripts package:dynOmics R Documentation
_<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Simulated data were received from Redestig et al., 2011.
Metabolite and transcript levels were obtained using an impulse
model (Chechik and Koller, 2009). Functions were used to model
five different metabolite patterns and for each metabolite 50
associated transcript levels. Time lags were introduced in the
range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
Simulated profiles have seven time points and normal distributed
noise was introduced with mean zero and standard deviation 0.1.
_<08>U_<08>s_<08>a_<08>g_<08>e:
data(Transcripts)
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
This data set contains the simulated expression 250 transcripts
for 7 time points.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
• Transcripts. data matrix with 7 rows and 250 columns. Each
row represents an experimental time sample, and each column a
single transcript.
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
The Transcript Simulation Data is based on the the paper of
Redestig _et al._ (2011).
_<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
Redestig,H. and Costa,I.G. Detection and interpretation of
metabolite-transcript coresponses using combined profiling data.
_Bioinformatics_ *27*(13) (2011), pp. i357 65.
Warning: Removed 126 row(s) containing missing values (geom_path).
Loading required package: lmms
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'lmms'
Installing package into '/tmp/RtmpMdaWnm/RLIBS_186e78023be'
(as 'lib' is unspecified)
Quitting from lines 168-177 (DynOmicsUserManual.Rmd)
Error: processing vignette 'DynOmicsUserManual.Rmd' failed with diagnostics:
trying to use CRAN without setting a mirror
--- failed re-building ‘DynOmicsUserManual.Rmd’
SUMMARY: processing the following file failed:
‘DynOmicsUserManual.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86
Version: 1.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘DynOmicsUserManual.Rmd’ using knitr
Loading required package: ggplot2
dynOmics-package package:dynOmics R Documentation
_<08>F_<08>a_<08>s_<08>t _<08>F_<08>o_<08>u_<08>r_<08>i_<08>e_<08>r _<08>t_<08>r_<08>a_<08>n_<08>s_<08>f_<08>o_<08>r_<08>m _<08>t_<08>o _<08>e_<08>s_<08>t_<08>i_<08>m_<08>a_<08>t_<08>e _<08>d_<08>e_<08>l_<08>a_<08>y_<08>s _<08>i_<08>n _<08>e_<08>x_<08>p_<08>r_<08>e_<08>s_<08>s_<08>i_<08>o_<08>n _<08>i_<08>n_<08>i_<08>t_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n _<08>t_<08>o
_<08>i_<08>d_<08>e_<08>n_<08>t_<08>i_<08>f_<08>y _<08>a_<08>s_<08>s_<08>o_<08>c_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n_<08>s _<08>b_<08>e_<08>t_<08>w_<08>e_<08>e_<08>n _<08>t_<08>i_<08>m_<08>e _<08>c_<08>o_<08>u_<08>r_<08>s_<08>e '_<08>o_<08>m_<08>i_<08>c_<08>s' _<08>d_<08>a_<08>t_<08>a.
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
The package provides functions to identify associations within one
or between two time course 'omics' data and visualise the
associations : associateData to estimate the delays and identify
associations of data sets containing time course 'omics'
experiments; plot.associations: to visualise associated profiles.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
Package: dynOmics
Type: Package
Version: 1.2
Date: 2018-06-12
License: GPL-2
LazyLoad: yes
Functions for associating data: 'associateData'
Functions for summarization: 'summary.associations'
Functions for plots: 'plot.associations'
_<08>A_<08>u_<08>t_<08>h_<08>o_<08>r(_<08>s):
Jasmin Straube with contributions from Kim-Anh Le Cao, Emma Huang
and Anne Bernard
Maintainer: Jasmin Straube <j.straube@qimrberghofer.edu.au>
Metabolites package:dynOmics R Documentation
_<08>M_<08>e_<08>t_<08>a_<08>b_<08>o_<08>l_<08>i_<08>t_<08>e _<08>a_<08>n_<08>d _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Simulated data were received from Redestig et al., 2011.
Metabolite and transcript levels were obtained using an impulse
model (Chechik and Koller, 2009). Functions were used to model
five different metabolite patterns and for each metabolite 50
associated transcript levels. Time lags were introduced in the
range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
Simulated profiles have seven time points and normal distributed
noise was introduced with mean zero and standard deviation 0.1.
_<08>U_<08>s_<08>a_<08>g_<08>e:
data(Metabolites)
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
This data set contains the simulated expression of 5 metabolites
for 7 time points.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
• Metabolites. data matrix with 7 rows and 5 columns. Each row
represents an experimental time sample, and each column a
single metabolite.
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
The Metabolite Simulation Data is based on the the paper of
Redestig _et al._ (2011).
_<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
Redestig,H. and Costa,I.G. Detection and interpretation of
metabolite-transcript coresponses using combined profiling data.
_Bioinformatics_ *27*(13) (2011), pp. i357 65.
Transcripts package:dynOmics R Documentation
_<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Simulated data were received from Redestig et al., 2011.
Metabolite and transcript levels were obtained using an impulse
model (Chechik and Koller, 2009). Functions were used to model
five different metabolite patterns and for each metabolite 50
associated transcript levels. Time lags were introduced in the
range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
Simulated profiles have seven time points and normal distributed
noise was introduced with mean zero and standard deviation 0.1.
_<08>U_<08>s_<08>a_<08>g_<08>e:
data(Transcripts)
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
This data set contains the simulated expression 250 transcripts
for 7 time points.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
• Transcripts. data matrix with 7 rows and 250 columns. Each
row represents an experimental time sample, and each column a
single transcript.
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
The Transcript Simulation Data is based on the the paper of
Redestig _et al._ (2011).
_<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
Redestig,H. and Costa,I.G. Detection and interpretation of
metabolite-transcript coresponses using combined profiling data.
_Bioinformatics_ *27*(13) (2011), pp. i357 65.
Warning: Removed 126 row(s) containing missing values (geom_path).
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