extractBackground: Background Motif Extraction

Description Usage Arguments Details Value Author(s) Examples

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

1
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 (jakewozniak@gmail.com)

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
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.