HMMcopy-input: WIG Import Functions
In HMMcopy: Copy number prediction with correction for GC and mappability bias for HTS data

Description Usage Arguments Details Value Author(s) References See Also Examples

Fast fixedStep WIG file reading and parsing

1 2	wigToRangedData(wigfile, verbose = TRUE) wigToArray(wigfile, verbose = TRUE)

`wigfile`	Filepath to fixedStep WIG format file
`verbose`	Set to FALSE to suppress messages

Reads the entire file into memory, then processes the file in rapid fashion, thus performance will be limited by memory capacity.

The WIG file is expected to conform to the minimal fixedStep WIG format (see References), where each chromsome is started by a “fixedStep” declaration line. The function assumes only a single track in the WIG file, and will ignore any lines before the first line starting with “fixedStep”.

RangedData for wigToRangedData with chromosome and position information, sorted in decreasing chromosal size and increasing position.

Numeric array for wigToArray sorted in decreasing chromosal size and increasing position.

Daniel Lai

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

wigsToRangedData is a wrapper around these functions for easy WIG file loading and structure formatting.

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  wigfile <- system.file("extdata", "tumour.wig", package = "HMMcopy")
  posAndValues <- wigToRangedData(wigfile)
  justValues <- wigToArray(wigfile)

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: geneplotter
Loading required package: Biobase
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    'browseVignettes()'. To cite Bioconductor, see
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Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: XML
Slurping: /usr/local/lib/R/site-library/HMMcopy/extdata/tumour.wig
Parsing: fixedStep chrom=6 start=1 step=10000 span=10000
Sorting by decreasing chromosome size
Slurping: /usr/local/lib/R/site-library/HMMcopy/extdata/tumour.wig
Parsing: fixedStep chrom=6 start=1 step=10000 span=10000
Sorting by decreasing chromosome size