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Last data update: 2014.03.03

R: Parameter validation for the 'findConsensusPeakRegions'...

findConsensusPeakRegionsValidation

R Documentation

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.

Author(s)

Astrid Deschenes

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(consensusSeekeR)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: BiocParallel
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/consensusSeekeR/findConsensusPeakRegionsValidation.Rd_%03d_medium.png", width=480, height=480)
> ### Name: findConsensusPeakRegionsValidation
> ### Title: Parameter validation for the 'findConsensusPeakRegions' function
> ### Aliases: findConsensusPeakRegionsValidation
> ### Keywords: internal
> 
> ### ** 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)
[1] 0
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>

Parameter validation for the findConsensusPeakRegions function