run.seqgl: SeqGL pipeline

Description Usage Arguments Details

Description

SeqGL pipeline

Usage

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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.