consensusSeekeR (version 1.0.2)

findConsensusPeakRegionsValidation: Parameter validation for the findConsensusPeakRegions function

Description

Validation of all parameters needed by the public findConsensusPeakRegions function.

Usage

findConsensusPeakRegionsValidation(narrowPeaks, peaks, chrList, extendingSize, expandToFitPeakRegion, shrinkToFitPeakRegion, minNbrExp, nbrThreads)

Arguments

narrowPeaks

a GRanges representing called peaks of signal for all experiments.

peaks

a GRanges representing peaks for all experiments.

chrList

a Seqinfo containing the name and the length of the chromosomes to analyze which indicate that all chromosomes must be analyzed.

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 consensus 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 region of the peak closest to the peaks median position for each experiment.

shrinkToFitPeakRegion

a logical indicating if the region size, which is set by the extendingSize parameter is shrinked to fit the narrow peak regions of the peaks when all those regions are smaller than the consensus region.

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.

nbrThreads

a numeric indicating the number of threads to use in parallel.

Value

0 indicating that all parameters validations have been successful.

Examples

## Loading datasets
data(A549_FOSL2_01_NarrowPeaks_partial)
data(A549_FOXA1_01_NarrowPeaks_partial)
data(A549_FOSL2_01_Peaks_partial)
data(A549_FOXA1_01_Peaks_partial)

## Assigning experiment name to each row of the dataset.
## NarrowPeak and Peak datasets from the same experiment must
## have identical names.
names(A549_FOXA1_01_Peaks_partial) <- rep("FOXA1_01",
                        length(A549_FOXA1_01_Peaks_partial))
names(A549_FOXA1_01_NarrowPeaks_partial) <- rep("FOXA1_01",
                        length(A549_FOXA1_01_NarrowPeaks_partial))
names(A549_FOSL2_01_Peaks_partial) <- rep("FOSL2_01",
                        length(A549_FOSL2_01_Peaks_partial))
names(A549_FOSL2_01_NarrowPeaks_partial) <- rep("FOSL2_01",
                        length(A549_FOSL2_01_NarrowPeaks_partial))

chrList <- Seqinfo("chr10", 135534747, NA)

consensusSeekeR:::findConsensusPeakRegionsValidation(
    narrowPeaks = c(A549_FOXA1_01_NarrowPeaks_partial,
            A549_FOSL2_01_NarrowPeaks_partial),
    peaks = c(A549_FOXA1_01_Peaks_partial,
            A549_FOSL2_01_Peaks_partial),
    chrList = chrList,
    extendingSize = 110,
    expandToFitPeakRegion = FALSE,
    shrinkToFitPeakRegion = TRUE,
    minNbrExp = 2,
    nbrThreads = 1)