Detection of cross-hybridization events in microarray experiments

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Documentation for package ‘crosshybDetector’ version 1.0.4

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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