Parsing and sorting of uncorrected read and sequence information files

Description

Loads WIG files for readcount, GC, and mappability data for non-overlapping windows of fixed length (i.e. bins), and returns a structure ready to used for readcount correction. See Details for specifics about file assumptions.

Usage

wigsToRangedData(readfile, gcfile, mapfile, verbose = FALSE)

Arguments

Details

The number of lines in the three input files are expected to be identical, although the order and names of chromsomes in the file need not be identical. Chromosome lengths are required to be identical and unique, and if the latter is not true, the order of the chromosomes must then be identical.

At present, these three WIG files are expected to be generated by external programs, namely those from the HMMcopy suite (see See Also), rather than by existing R packages out of space and memory considerations when working with high coverage full genome samples.

Value

A RangedData object, where each row entry represents a bin, with the three values from the input as columns named reads, gc, and map.

Author(s)

Daniel Lai

References

correctedReadcount Suite

TBA

WIG

http://genome.ucsc.edu/goldenPath/help/wiggle.html

See Also

correctReadcount, to correct the readcounts in the resultant value.

Examples

rfile <- system.file("extdata", "tumour.wig", package = "HMMcopy")
gfile <- system.file("extdata", "gc.wig", package = "HMMcopy")
mfile <- system.file("extdata", "map.wig", package = "HMMcopy")

uncorrected_reads <- wigsToRangedData(rfile, gfile, mfile)

Results

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> library(HMMcopy)
Loading required package: IRanges
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: geneplotter
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")'.

Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: XML
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/HMMcopy/wigsToRangedData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: wigsToRangedData
> ### Title: Parsing and sorting of uncorrected read and sequence information
> ###   files
> ### Aliases: wigsToRangedData
> ### Keywords: IO
> 
> ### ** Examples
> 
> 
> rfile <- system.file("extdata", "tumour.wig", package = "HMMcopy")
> gfile <- system.file("extdata", "gc.wig", package = "HMMcopy")
> mfile <- system.file("extdata", "map.wig", package = "HMMcopy")
> 
> uncorrected_reads <- wigsToRangedData(rfile, gfile, mfile)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>