crosshybDetector-package |
Detection of cross-hybridization events in microarray experiments
|
AAAlignment-class |
"AAAlignment" result of pairwise sequence alignment. |
AAAlphabet-class |
Class "AAAlphabet" Amino Acid Alphabet |
AASequence |
AASequence constructor |
AASequence-class |
"AASequence" Object representation of a protein Sequence |
AASequenceList-class |
Class "AASequenceList" - Container |
computeTm |
Computing of melting temperature |
crosshyb |
Identify probes affected by crosshybridization |
crosshyb.out |
Output of crosshyb |
crosshyb2xls |
Write corruptor and corrupted probes to files |
crosshyb2xls.putative |
Writing list of analyzed probes to file |
crosshybDetector |
Detection of cross-hybridization events in microarray experiments
|
crosshybImage |
Spatial distribution of corruptor and corrupted probes |
crosshybMAplot |
MA-plot |
crosshybMCplot |
Plot of Monte Carlo simulations |
crosshyb_func |
Computing cross-hybrization pvalues |
EBLOSUM50 |
Amino Acid Substitution matrices |
EBLOSUM62 |
Amino Acid Substitution matrices |
EPAM110 |
Amino Acid Substitution matrices |
extractBadProbes |
Extract corruptor and corrupted probes |
frequency,AASequence-method |
"AASequence" Object representation of a protein Sequence |
getSeqs |
Read sequences |
infogrep |
reader for databases in Fasta file format. |
initialize,AASequence-method |
"AASequence" Object representation of a protein Sequence |
levels,AAAlphabet-method |
Class "AAAlphabet" Amino Acid Alphabet |
list2ascii |
Write R list |
listdist |
Compute distance matrix from a list |
listdist,list-method |
Compute distance matrix from a list |
listdist-methods |
Compute distance matrix from a list |
probeSeq |
Sequence data |
raw |
marrayRaw example data |
readFasta |
reader for databases in Fasta file format. |
readFasta,AASequence-method |
reader for databases in Fasta file format. |
readFasta,AASequenceList-method |
reader for databases in Fasta file format. |
readFasta-methods |
reader for databases in Fasta file format. |
rg2ma |
Convert intensities to ratios |
salign |
Optimal pairwise alignment of two protein sequences. |
salign,AASequence,AASequence-method |
Optimal pairwise alignment of two protein sequences. |
salign,AASequence,AASequenceList-method |
Optimal pairwise alignment of two protein sequences. |
salign,AASequenceList,AASequence-method |
Optimal pairwise alignment of two protein sequences. |
salign,AASequenceList,NULL-method |
Optimal pairwise alignment of two protein sequences. |
salign-methods |
Optimal pairwise alignment of two protein sequences. |
selfalign |
"AASequence" Object representation of a protein Sequence |
selfalign,AASequence,Submatrix-method |
"AASequence" Object representation of a protein Sequence |
seqgrep |
reader for databases in Fasta file format. |
show,AAAlignment-method |
"AAAlignment" result of pairwise sequence alignment. |
show,AAAlphabet-method |
Class "AAAlphabet" Amino Acid Alphabet |
show,AASequence-method |
"AASequence" Object representation of a protein Sequence |
show,AASequenceList-method |
Class "AASequenceList" - Container |
show,Submatrix-method |
Class "Submatrix" Substitution Matrix |
subFromEmboss |
Class "Submatrix" Substitution Matrix |
subFromEmboss,Submatrix,character-method |
Class "Submatrix" Substitution Matrix |
Submatrix |
Class "Submatrix" Substitution Matrix |
Submatrix-class |
Class "Submatrix" Substitution Matrix |
summary,AAAlignment-method |
"AAAlignment" result of pairwise sequence alignment. |
testalign |
Scoring of optimal alingments. |
testalign,AASequence,AASequence-method |
Scoring of optimal alingments. |
testalign-methods |
Scoring of optimal alingments. |
[,AASequenceList-method |
Class "AASequenceList" - Container |
[<-,AASequenceList-method |
Class "AASequenceList" - Container |
[[<-,AASequenceList-method |
Class "AASequenceList" - Container |