runMotifRG: runMotifRG

Description Usage Arguments Value Examples

View source: R/motif_analysis.R

Description

This function makes use of motifRG library to carry out de novo motif discovery from input query regions

Usage

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runMotifRG(queryRegions, resizeN = 0, sampleN = 0, genomeVersion,
  motifN = 5, nCores = 4)

Arguments

queryRegions

GRanges object containing coordinates of input query regions imported by the importBed function

resizeN

Integer value (default: 0) to resize query regions if they are shorter than the value of resize. Set to 0 to disable resize.

sampleN

A positive integer value. The queryRegions are randomly downsampled to include intervals as many as sampleN. The input will be downsampled only if this value is larger than zero and less than the total number of input intervals.

genomeVersion

A character string to denote the BS genome library required to extract sequences. Available options are hg19, mm9, ce10 and dm3.

motifN

A positive integer (default:5) denoting the maximum number of motifs that should be sought by the motifRG::findMotifFgBg function

nCores

A positive integer (default:4) number of cores used for parallel execution.

Value

a list of objects returned by the motifRG::findMotif function

Examples

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data(queryRegions)
motifResults <- runMotifRG(queryRegions = queryRegions,
                          genomeVersion = 'hg19',
                          resize = 15,
                          motifN = 1,
                          nCores = 2)

RCAS documentation built on Nov. 1, 2018, 2:54 a.m.