cleanPeptides: clean up peptides

Description Usage Arguments Value Author(s) Examples

View source: R/cleanPeptides.R

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

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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

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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.