extractBackground: Background Motif Extraction

In jmwozniak/PTMphinder: An R package for PTM localization and motif extraction from 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

# Locate example files
examples.path = system.file("extdata", package = "PTMphinder")
parsed_ref.path = paste(examples.path, "/Human_Uniprot_Parsed_Example.txt", sep="")

# Read in parsed Uniprot database example (or one you created with parseDB above)
parsed_ref <- read.table(parsed_ref.path, header=FALSE, row.names=NULL, sep="\t")

# Set parameters for extractBackground (s - sequence list; c - central character; w - width of motifs)
s <- unlist(parsed_ref[,2])
c <- "S"
w <- 15

# Extract proteome-specific background motifs (may take a while depending on database size)
extractBack_Example <- extractBackground(s, c, w)

# Create file name for background motif list
fileName2 <- paste(examples.path, "/Background_", c, "_" ,w, "_", Sys.Date(), ".txt", sep="")

# Write background motif list to new file (will be found in the PTMphinder/extdata/ directory within R.framework)
write.table(extractBack_Example, fileName2, row.names=FALSE, col.names=FALSE, quote=FALSE)

jmwozniak/PTMphinder documentation built on May 31, 2019, 10:34 a.m.