run.seqgl: SeqGL pipeline

In ManuSetty/SeqGL: Group lasso for Dnase/ChIP-seq data

Description

SeqGL pipeline

Usage

run.seqGL(peaks.file, out.dir, data.type, org, span = 150,
  max.examples = ifelse(data.type == "ChIP", 5000, 40000), no.cores = 1,
  no.groups = ifelse(data.type == "ChIP", 20, 100),
  dictionary.file = system.file("extdata/wildcard_dict_kmer8_mismatches2_alpha5_consecutive_mis.Rdata",
  package = "SeqGL"))

Arguments

peaks.file	Bed file containing the peaks. See Details.
out.dir	Path to the output directory
data.type	ChIP or DNase: indicating the experiment though which the peaks were derived
org	IUPAC organism code. hg19, hg18, mm10, mm9, mm8 are supported. Note that the corresponding BSGenome package has to be installed.
span	Width of the peaks used for analysis. Default is 150
no.cores	Number of cores for parallel processing
no.groups	Number of groups to use for group lasso
dictionary.file	The positional wildcard dictionary file built using ChIPKernel. A dicionary will be built if it not specified.
max.exmamples	Maximum examples for training. Note that group membership will be determined for all examples

Details

SeqGL results will be available in out.dir

ManuSetty/SeqGL documentation built on March 14, 2021, 3:18 a.m.