calcGC2: Calculate GC Percentage in sliding window

In genoset: A RangedSummarizedExperiment with methods for copy number analysis

Description

Local GC content can be used to remove GC artifacts from copynumber data (see Diskin et al, Nucleic Acids Research, 2008, PMID: 18784189). This function will calculate GC content fraction in expanded windows around a set of ranges following example in http://www.bioconductor.org/help/course-materials/2012/useR2012/Bioconductor-tutorial.pdf. Values are as.integer( 1e4 * fraction ) for space reasons.

Usage

calcGC2(dna)

Arguments

dna	BSgenome or DNAStringSet

Value

SimpleRleList, integer 1e4 * GC fraction, chromosomes 1:22, X and Y

Examples

## Not run:  library(BSgenome.Hsapiens.UCSC.hg19) 
## Not run:  gc = calcGC2(Hsapiens) 

Example output

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: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
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: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    apply

genoset documentation built on Nov. 8, 2020, 6:07 p.m.