WIG Output Functions

Description

Fast fixedStep WIG file formatting and output

Usage

rangedDataToWig(correctOutput, file, column = "copy", sample = "R",
  verbose = TRUE)
rangedDataToSeg(correctOutput, file, column = "copy", sample = "R",
  verbose = TRUE)

Arguments

Details

Assumes that all ranges in data set are non-overlapping windows of fixed width covering the entire genome. Note that positions in WIG files are 1-based while those in SEG files are 0-based.

Author(s)

Daniel Lai

References

WIG

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

SEG

http://www.broadinstitute.org/igv/SEG

See Also

correctReadcount output is the intended input

Examples

  data(tumour) # Load tumour_copy
  rangedDataToWig(tumour_copy, file = "test.wig")
  rangedDataToSeg(tumour_copy, file = "test.seg")

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 'demo()' for some demos, 'help()' for on-line help, or
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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/HMMcopy-output.Rd_%03d_medium.png", width=480, height=480)
> ### Name: WIG Output Functions
> ### Title: WIG Output Functions
> ### Aliases: rangedDataToWig rangedDataToSeg
> ### Keywords: IO
> 
> ### ** Examples
> 
>   data(tumour) # Load tumour_copy
>   rangedDataToWig(tumour_copy, file = "test.wig")
Outputting chromosome 6 (4273)
>   rangedDataToSeg(tumour_copy, file = "test.seg")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>