annotatePeaks.pl: annotatePeaks.pl

In avhgenomics/bioKIT: bioKIT: Common functions for routine molecular biology applications.

Description

builds a command to run Homer's annotatePeaks.pl with a set of commonly used flags.

Usage

annotatePeaks.pl(bedfile, genome = "mm10", specific_motifs = NULL,
  mscore = F, mbed = NULL, center = NULL, annStats = NULL, outputfile,
  run_as_sys = F, win_sys = F)

Arguments

bedfile	The full path to the bed file
genome	the genome to use; "mm10" is default.
specific_motifs	Search for specific motifs? Takes a vector; adds the "-m" flag.
mscore	Requires specific_motifs; returns log-odds score. logical.
mbed	return specific locations of the motifs found. argument takes the string of the full path to the output bed file.
center	Center on a motif? argument takes the string of the full path to the output bed file.
annStats	Returns a detailed set of annotation statistics. argument takes the string of the full path to the output txt file.
outputfile	Full path to the annotated output text file.
run_as_sys	run this command through system? False by default, returning the command string.
win_sys	Set to False; this enables the system command to work properly on windows.

Value

By default, this returns a string of the compiled command. If run_as_sys == T, this will run the command as well.

Examples

# annotatePeaks.pl(bedfile = "example.bed",genome = "mm10",outputfile = "annotated_output.txt")

avhgenomics/bioKIT documentation built on May 5, 2019, 12:29 a.m.