plotCleavageMatrix: Plot cleavage site matrix from identified peptide sequences

Description Usage Arguments Value See Also Examples

View source: R/plotCleavageMatrix.R

Description

This function allows to examine specificity of enzymatic digestion (or chemical cleavage) at dipeptide sequence level, based on MS/MS identification result (search without any enzyme specification, or "unspecific" search). Can be useful to check cleavage selectivity & efficiency of each enzyme used in multiple digestion or of less-specific enzymes.

Usage

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plotCleavageMatrix(seq, after, hide.plot = FALSE, normalize = FALSE,
  col.regions = NULL)

Arguments

seq

A character vector of identified peptide sequences without any modifications. Should only made up of 20 amino acids one letter characters.

after

A character vector of peptide sequences after cleavage site. Only the first amino acid is used, but can be of longer length.

hide.plot

Logical, default FALSE. If set to TRUE, no plot will be drawn. Can be used just to obtain a data.frame of cleavage site frequency for manual plotting.

normalize

Logical, default FALSE (stacked barchart of cleaved and not-cleaved).

col.regions

Color palette function like heat.colors etc.

Value

If assigned to a variable, this function returns a cleavage site matrix, with its row being the first amino acid and its column being the second amino acid.

See Also

plotCleavage, extractDCasMat

Examples

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data(LysCTryp)
plotCleavageMatrix(LysCTryp$Sequence, LysCTryp$AAs.After, normalize=TRUE)

ohgane/DigestionSpecificity documentation built on May 23, 2017, 7:09 p.m.