Fast fixedStep WIG file reading and parsing
Filepath to fixedStep WIG format file
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”.
wigToRangedData with chromosome and position information, sorted
in decreasing chromosal size and increasing position.
sorted in decreasing chromosal size and increasing position.
wigsToRangedData is a wrapper around these functions for easy
WIG file loading and structure formatting.
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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 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 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
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