Tools for analysing OmniLog(R) Phenotype Microarray data


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Documentation for package ‘opm’ version 0.8-0

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A B C D E F G H I K L M O P R S T U V W X Y misc

opm.package-package The opm package

-- A --

aggregated Get aggregated kinetic data
aggregated-method Get aggregated kinetic data
aggregated-methods Get aggregated kinetic data
aggr_settings Get aggregation settings
aggr_settings-method Get aggregation settings
aggr_settings-methods Get aggregation settings
anyDuplicated Determine whether plates are duplicated
anyDuplicated-method Determine whether plates are duplicated
anyDuplicated-methods Determine whether plates are duplicated

-- B --

batch_collect Collect information from files
batch_opm_to_yaml Batch-convert to YAML
batch_process Convert infiles to outfiles
best_cutoff Determine best cutoff
best_cutoff-method Determine best cutoff
best_cutoff-methods Determine best cutoff
borders Cluster borders
borders.Ckmeans.1d.dp Cluster borders
borders.kmeans Cluster borders
borders.kmeanss Cluster borders
bracket-method Select subset
bracket-methods Select subset

-- C --

c Combination
c-method Combination
c-methods Combination
calinski Calinski-Harabasz statistics
calinski.Ckmeans.1d.dp Calinski-Harabasz statistics
calinski.kmeans Calinski-Harabasz statistics
calinski.kmeanss Calinski-Harabasz statistics
ci_plot Plot point estimates with CIs
ci_plot-method Plot point estimates with CIs
ci_plot-methods Plot point estimates with CIs
clean_filenames Clean file names
collect_template Collect metadata template
collect_template-method Collect metadata template
collect_template-methods Collect metadata template
contains Query a list with a list
contains-method Query a list with a list
contains-methods Query a list with a list
csv_data Information from input CSV file
csv_data-method Information from input CSV file
csv_data-methods Information from input CSV file

-- D --

dim Dimensions
dim-method Dimensions
dim-methods Dimensions
discrete Convert to discrete characters
discrete-method Convert to discrete characters
discrete-methods Convert to discrete characters
discretized Get discretized kinetic data
discretized-method Get discretized kinetic data
discretized-methods Get discretized kinetic data
disc_settings Get discretization settings
disc_settings-method Get discretization settings
disc_settings-methods Get discretization settings
do_aggr Aggregate kinetics using curve-parameter estimation
do_aggr-method Aggregate kinetics using curve-parameter estimation
do_aggr-methods Aggregate kinetics using curve-parameter estimation
do_disc Discretize curve parameters
do_disc-method Discretize curve parameters
do_disc-methods Discretize curve parameters
duplicated Determine duplicated plates
duplicated-method Determine duplicated plates
duplicated-methods Determine duplicated plates

-- E --

explode_dir Conversion of directory names to file names
extract Extract aggregated values
extract-method Extract aggregated values
extract-methods Extract aggregated values
extract_columns Create data frame or vector from metadata
extract_columns-method Create data frame or vector from metadata
extract_columns-methods Create data frame or vector from metadata

-- F --

fast_estimate Fast curve-parameter estimation
fast_estimate-method Fast curve-parameter estimation
fast_estimate-methods Fast curve-parameter estimation
filename Original input filename
filename-method Original input filename
filename-methods Original input filename
file_pattern File pattern
find_positions Identify positions of substrates
find_positions-method Identify positions of substrates
find_positions-methods Identify positions of substrates
find_substrate Identify substrates
find_substrate-method Identify substrates
find_substrate-methods Identify substrates
flatten Flatten measurements from OPM or OPMS objects
flatten-method Flatten measurements from OPM or OPMS objects
flatten-methods Flatten measurements from OPM or OPMS objects

-- G --

gen_iii Change to Generation III (or other plate type)
gen_iii-method Change to Generation III (or other plate type)
gen_iii-methods Change to Generation III (or other plate type)
glob_to_regex Convert wildcard to regular expression
glob_to_regex-method Convert wildcard to regular expression
glob_to_regex-methods Convert wildcard to regular expression

-- H --

has_aggr Are aggregated data present?
has_aggr-method Are aggregated data present?
has_aggr-methods Are aggregated data present?
has_disc Are discretized data present?
has_disc-method Are discretized data present?
has_disc-methods Are discretized data present?
heat_map Heat map
heat_map-method Heat map
heat_map-methods Heat map
hist.Ckmeans.1d.dp Cluster borders
hist.kmeans Cluster borders
hist.kmeanss Cluster borders
hours Overall measuring hours
hours-method Overall measuring hours
hours-methods Overall measuring hours
html_args Default HTML formatting arguments

-- I --

include_metadata Add metadata (from file or data frame)
include_metadata-method Add metadata (from file or data frame)
include_metadata-methods Add metadata (from file or data frame)
infix.k Search in metadata keys
infix.k-method Search in metadata keys
infix.k-methods Search in metadata keys
infix.largek Search in metadata keys
infix.largek-method Search in metadata keys
infix.largek-methods Search in metadata keys
infix.largeq Query metadata (strict version)
infix.largeq-method Query metadata (strict version)
infix.largeq-methods Query metadata (strict version)
infix.q Query metadata (non-exact version)
infix.q-method Query metadata (non-exact version)
infix.q-methods Query metadata (non-exact version)

-- K --

kubrick Stanley Kubrick

-- L --

length OPMS length (number of plates)
length-method OPMS length (number of plates)
length-methods OPMS length (number of plates)
level_plot Levelplot
level_plot-method Levelplot
level_plot-methods Levelplot
listing Create textual listing
listing-method Create textual listing
listing-methods Create textual listing

-- M --

map_metadata Map metadata
map_metadata-method Map metadata
map_metadata-methods Map metadata
map_names Map names
map_names-method Map names
map_names-methods Map names
map_values Map values
map_values-method Map values
map_values-methods Map values
max Maximum
max-method Maximum
max-methods Maximum
measurements Stored measurements
measurements-method Stored measurements
measurements-methods Stored measurements
merge Merge plates
merge-method Merge plates
merge-methods Merge plates
metadata Get metadata
metadata-method Get metadata
metadata-methods Get metadata
metadata.set Replace metadata
metadata.set-method Replace metadata
metadata.set-methods Replace metadata
metadata<- Replace metadata
metadata<--method Replace metadata
metadata_chars Get metadata characters
metadata_chars-method Get metadata characters
metadata_chars-methods Get metadata characters
minmax Smallest maximum
minmax-method Smallest maximum
minmax-methods Smallest maximum
MOA MOA class
MOA-class MOA class

-- O --

oapply Apply method for OPMS objects
oapply-method Apply method for OPMS objects
oapply-methods Apply method for OPMS objects
OPM OPM class
OPM-class OPM class
opm.package The opm package
OPMA OPMA class
OPMA-class OPMA class
OPMD OPMD class
OPMD-class OPMD class
OPMS OPMS class
opms OPMS constructor
OPMS-class OPMS class
OPMX OPMX class
OPMX-class OPMX class
opm_files Opm files
opm_opt OPM options
opm_opt-method OPM options
opm_opt-methods OPM options

-- P --

param_names Names of curve parameters
phylo_data Export phylogenetic data
phylo_data-method Export phylogenetic data
phylo_data-methods Export phylogenetic data
plates Get available plates
plates-method Get available plates
plates-methods Get available plates
plate_type Plate type used or normalized
plate_type-method Plate type used or normalized
plate_type-methods Plate type used or normalized
plot.kmeanss Calinski-Harabasz statistics
plus Addition
plus-method Addition
plus-methods Addition
position Position of a plate
position-method Position of a plate
position-methods Position of a plate

-- R --

radial_plot Radial plot
radial_plot-method Radial plot
radial_plot-methods Radial plot
read_opm Read multiple PM files at once
read_single_opm Read single PM file
rep Repeat OPMS objects
rep-method Repeat OPMS objects
rep-methods Repeat OPMS objects
rev Revert OPMS objects
rev-method Revert OPMS objects
rev-methods Revert OPMS objects
run_kmeans Conduct k-means partitioning
run_kmeans-method Conduct k-means partitioning
run_kmeans-methods Conduct k-means partitioning

-- S --

safe_labels Safe labels
select Select a subset of the plates (or time points) [deprecated]
select-method Select a subset of the plates (or time points) [deprecated]
select-methods Select a subset of the plates (or time points) [deprecated]
select_colors Select colours
separate Regularly split character vectors if possible
separate-method Regularly split character vectors if possible
separate-methods Regularly split character vectors if possible
seq Sequence of plate indexes
seq-method Sequence of plate indexes
seq-methods Sequence of plate indexes
setup_time Setup time of the measuring
setup_time-method Setup time of the measuring
setup_time-methods Setup time of the measuring
show Show OPM or OPMS objects
show-method Show OPM or OPMS objects
show-methods Show OPM or OPMS objects
sort Sort OPMS objects
sort-method Sort OPMS objects
sort-methods Sort OPMS objects
split_files Split files
subset Select a subset of the plates (or time points)
subset-method Select a subset of the plates (or time points)
subset-methods Select a subset of the plates (or time points)
substrate_info Provide information on substrates
substrate_info-method Provide information on substrates
substrate_info-methods Provide information on substrates
summary Summarize OPM or OPMS objects
summary-method Summarize OPM or OPMS objects
summary-methods Summarize OPM or OPMS objects

-- T --

thin_out Thin out the measurements
thin_out-method Thin out the measurements
thin_out-methods Thin out the measurements
to_kmeans Convert to kmeans
to_kmeans.Ckmeans.1d.dp Convert to kmeans
to_kmeans.kmeans Convert to kmeans
to_kmeans.kmeanss Convert to kmeans
to_metadata Input metadata
to_metadata-method Input metadata
to_metadata-methods Input metadata
to_yaml Convert to YAML
to_yaml-method Convert to YAML
to_yaml-methods Convert to YAML

-- U --

unique Make OPMS objects unique
unique-method Make OPMS objects unique
unique-methods Make OPMS objects unique

-- V --

vaas_1 Example data set from Vaas et al. (2012), a single selected plate
vaas_4 Example data set from Vaas et al. (2012), four selected plates

-- W --

well Measurements from selected wells
well-method Measurements from selected wells
well-methods Measurements from selected wells
wells Available well names
wells-method Available well names
wells-methods Available well names
well_to_substrate Map well names to substrates
WMD WMD class
WMD-class WMD class

-- X --

xy_plot XY plot
xy_plot-method XY plot
xy_plot-methods XY plot

-- Y --

YAML_VIA_LIST YAML_VIA_LIST class
YAML_VIA_LIST-class YAML_VIA_LIST class

-- misc --

%K% Search in metadata keys
%k% Search in metadata keys
%K%-method Search in metadata keys
%k%-method Search in metadata keys
%Q% Query metadata (strict version)
%q% Query metadata (non-exact version)
%Q%-method Query metadata (strict version)
%q%-method Query metadata (non-exact version)
+-method Addition
[ Select subset
[-method Select subset