cleanPeptides: clean up peptides

In dagLogo: dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory

Description

clean up the input peptide subsequences. The function removes peptides which do NOT contain any anchoring amino acid. Adds peptide for each additional anchor in each peptide, and allows multiple anchoring amino acids.

Usage

cleanPeptides(dat, anchors)

Arguments

dat	input data. The input dat contains two columns 'symbol', protein ID, and 'peptides', peptide sequence.The anchoring amino acid must be in lower case.
anchors	A vector of character, anchoring amino acid must be in lower case.

Value

A data.frame with columns: 'symbol', 'peptides' and 'anchor'

Author(s)

Jianhong Ou, Julie Zhu

Examples

dat <- read.csv(system.file("extdata", "peptides2filter.csv", package="dagLogo"))
dat
dat.new <- cleanPeptides(dat, anchors = c("s", "t"))

dagLogo documentation built on Dec. 5, 2020, 2 a.m.