findConsensusPeakRegionsForOneChrom: Extract regions sharing features in more than one experiment...

Description Usage Arguments Value Author(s)

View source: R/findConsensusPeakRegionsIntern.R

Description

Find regions sharing the same features for a minimum number of experiments using called peaks of signal enrichment based on pooled, normalized data (mainly coming from narrowPeak files). Tje analysis is limited to one chromosome. The peaks and narrow peaks are used to identify the consensus regions. The minimum number of experiments that must have at least on peak in a region so that it is retained as a consensus region is specified by user, as well as the size of mining regions.

Usage

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findConsensusPeakRegionsForOneChrom(chrName, allPeaks, allNarrowPeaks,
  extendingSize, expandToFitPeakRegion, shrinkToFitPeakRegion, minNbrExp,
  chrList)

Arguments

chrName

a character, the name of the chromosome to analyze.

allPeaks

a GRanges containing all peaks from all experiments sorted by position.

allNarrowPeaks

a GRanges containing all narrow peaks from all experiments sorted by position.

extendingSize

a numeric value indicating the size of padding at each side of the peaks median position to create the consensus region. The minimum size of the consensu region will be equal to twice the value of the extendingSize parameter. The size of the extendingSize must be a positive integer. Default = 250.

expandToFitPeakRegion

a logical indicating if the region set by the extendingSize parameter is extended to include all narrow peak regions. Only the narrow peaks regions of the peaks included in the unextended region are used during the extension process. It is possible that has a side effect, adding peaks are being included in the extended region.

shrinkToFitPeakRegion

a logical indicating if the region set by the extendingSize parameter is shrinked to fit the narrow peak regions.

minNbrExp

a numeric indicating the minimum number of BED files in which a peak must be present for a region to be retained. The numeric must be a positive value inferior or equal to the number of files present in the narrowPeakFiles parameter. Default = 1.

chrList

a Seqinfo containing the name and the length of the chromosomes to analyze.

Value

an object of class "commonFeatures".

Author(s)

Astrid Deschenes


ArnaudDroitLab/consensusSeekeR documentation built on Sept. 2, 2017, 8:25 p.m.