autoseed_motif_disc: Motif Discovery with Autoseed

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Motif Discovery with Autoseed

Description

Motif Discovery with Autoseed

Usage

autoseed_motif_disc(
  sig_file,
  outdir = NULL,
  bk_file = "/var/www/html/selex/data/sequence/Empty.seq",
  local_max_cutoff = 40
)

Arguments

sig_file	a file containing the reads for motif discovery, can be either a fastq, fasta, or plain text file
outdir	the path to store output data (seeds and svg visualizations)
bk_file	the background file for motif discovery, leave blank to use random sequences
local_max_cutoff	the sensitivity of motif discovery (it tells at least how many hits of the seed consensus should exist in the sig_file, in order to generate a PFM output for this seed )

Value

a list of pfms discovered from the sig_file, can use ggseqlogo for further visualization

Examples

sig_file="/var/www/html/selex/data/sequence/random40ND8.44.ATI4.seedling.root.20101n.1..30n4u_sig.seq"
result=autoseed_motif_disc(sig_file,"/wrk/zhu/test/autoseed_test",local_max_cutoff = 20)

hbmcsysbio/hbmcbioR documentation built on April 14, 2022, 9:59 p.m.