Subsample short read alignment locations

Description

Subsamples data from multiple lanes on a per-chromosome basis.

Usage

laneSubsample(lane1, lane2, fudge = 0.05)

Arguments

Value

laneSubsample returns a list similar to its input, but with the larger dataset subsampled to be similar to the smaller one.

Author(s)

D. Sarkar

Examples

data(cstest)
## subsample to compare lanes
cstest.sub <- laneSubsample(cstest[[1]], cstest[[2]])
unlist(cstest.sub)

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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> library(chipseq)
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: 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: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/chipseq/laneSubsample.Rd_%03d_medium.png", width=480, height=480)
> ### Name: laneSubsample
> ### Title: Subsample short read alignment locations
> ### Aliases: laneSubsample
> ### Keywords: manip utilities
> 
> ### ** Examples
> 
> data(cstest)
> ## subsample to compare lanes
> cstest.sub <- laneSubsample(cstest[[1]], cstest[[2]])
> unlist(cstest.sub)
GRanges object with 590770 ranges and 0 metadata columns:
        seqnames                 ranges strand
           <Rle>              <IRanges>  <Rle>
  lane1    chr10     [3012941, 3012964]      +
  lane1    chr10     [3012978, 3013001]      +
  lane1    chr10     [3013071, 3013094]      +
  lane1    chr10     [3023240, 3023263]      +
  lane1    chr10     [3038377, 3038400]      +
    ...      ...                    ...    ...
  lane2    chr12 [121213126, 121213149]      -
  lane2    chr12 [121216905, 121216928]      -
  lane2    chr12 [121216967, 121216990]      -
  lane2    chr12 [121251805, 121251828]      -
  lane2    chr12 [121253426, 121253449]      -
  -------
  seqinfo: 35 sequences from an unspecified genome
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>