Coverage calculation and normalization to reads per million (rpm)

Description

Calculates the coverage values from a RangedData object (or anything with a defined coverage function associated) and returns the coverage normalized to reads per million, allowing the comparison of experiments with a different absolut number of reads.

Usage

coverage.rpm(data, scale=1e6, ...)

Arguments

Value

RleList object with the coverage objects

Author(s)

Oscar Flores oflores@mmb.pcb.ub.es

See Also

processReads, coverage

Examples

	
	#Load the example dataset and get the coverage
	data(nucleosome_htseq)
	cov = coverage.rpm(nucleosome_htseq)

	print(cov)

	#Plot it
	plot(as.vector(cov[["chr1"]]), type="l", ylab="coverage", xlab="position")

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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Type 'q()' to quit R.

> library(nucleR)
Loading required package: ShortRead
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: BiocParallel
Loading required package: Biostrings
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: IRanges
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/nucleR/coverage.rpm.Rd_%03d_medium.png", width=480, height=480)
> ### Name: coverage.rpm
> ### Title: Coverage calculation and normalization to reads per million
> ###   (rpm)
> ### Aliases: coverage.rpm
> ### Keywords: manip
> 
> ### ** Examples
> 
> 	
> 	#Load the example dataset and get the coverage
> 	data(nucleosome_htseq)
> 	cov = coverage.rpm(nucleosome_htseq)
> 
> 	print(cov)
RleList of length 1
$chr1
numeric-Rle of length 8284 with 4589 runs
  Lengths:                4                1 ...                3
  Values : 55.5524693072607 277.762346536304 ... 222.209877229043

> 
> 	#Plot it
> 	plot(as.vector(cov[["chr1"]]), type="l", ylab="coverage", xlab="position")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>