extractBackground: Background Motif Extraction

In jmwozniak/PhosPhinder: An R package for phospho-site localization and motif extraction from phospho-proteomic datasets

Description

extractBackground() extracts a list of background sequences (of a particular width centered around a specific character) from an input file for subsequent use with tools such as motif-x.

Usage

extractBackground(sequences, central, width)

Arguments

sequences	list of sequences from which background will be extracted.
central	a character denoting the central residue for the background you want to extract (eg. S for Serine).
width	an integer denoting the width of the motif you want to extract.

Details

output will be limited to background sequences that are at least the size of the specified width. Background sequences that are shorter than this width (due to being near termini of proteins) will be removed.

Value

a list of strings

Author(s)

Jacob M. Wozniak ([e-mail])

Examples

require(PhosPhinder)

examples.path = system.file("extdata", package = "PhosPhinder")
parsed_ref.path = paste(examples.path, "/Human_Uniprot_Parsed_Example.txt", sep="")

parsed_ref <- read.table(parsed_ref.path, header=FALSE, row.names=NULL, sep="\t")

s <- unlist(parsed_ref[,2])
c <- "S"
w <- 15

extractBack_Example <- extractBackground(s, c, w)

fileName2 <- paste(examples.path, "/Background_", c, "_" ,w, "_", Sys.Date(), ".txt", sep="")

write.table(extractBack_Example, fileName2, row.names=FALSE, col.names=FALSE, quote=FALSE)

jmwozniak/PhosPhinder documentation built on May 30, 2019, 1:32 p.m.