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

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

Fast fixedStep WIG file formatting and output

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

`correctOutput`	`RangedData` object for output, default options expect output from `correctReadcount`.
`file`	Filepath to write output to.
`column`	Column in input object to export. Defaults to corrected copy number.
`sample`	Sample name of the exported dataset, defaults to “R”
`verbose`	Set to FALSE to suppress messages.

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.

Daniel Lai

WIG: http://genome.ucsc.edu/goldenPath/help/wiggle.html
SEG: http://www.broadinstitute.org/igv/SEG

correctReadcount output is the intended input

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

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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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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Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: XML
Outputting chromosome 6 (4273)