Count reads in nonoverlapping bins across a chromosome

Description

Stratify chromosome into nonoverlapping bins of the same size and count the number of reads that fall within each bin.

Usage

binCount(alignGR, binSize, returnBinCountOnly = FALSE)

Arguments

Details

The funciton is designed to operate to a single chromosome to facilitate parallel computing on multiple chromosomes independently. The function is used in evalBinSize to select the optimal bin size based on the read counts and in mainSeekSingleChrom to provide the read count as input for the HMM.

Value

If returnBinCountOnly is TRUE, then the integer read count is returned; if returnBinCountOnly is FALSE, then the GRanges of bins with value slot saved for the corresponding read counts is returned.

Author(s)

Yue Li

References

P. Aboyoun, H. Pages and M. Lawrence. GenomicRanges: Representation and manipulation of genomic intervals. R package version 1.8.9.

See Also

selectBinSize, evalBinSize

Examples

# Retrieve system files
extdata.dir <- system.file("extdata", package="RIPSeeker") 

bamFiles <- list.files(extdata.dir, ".bam$", recursive=TRUE, full.names=TRUE)

bamFiles <- grep("PRC2", bamFiles, value=TRUE)

alignGal <- getAlignGal(bamFiles[1], reverseComplement=TRUE, genomeBuild="mm9")

alignGR <- as(alignGal, "GRanges")

alignGRList <- GRangesList(as.list(split(alignGR, seqnames(alignGR))))

binSize <- 1000

binGR <- binCount(alignGRList$chrX, binSize)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(RIPSeeker)
Loading required package: S4Vectors
Loading required package: stats4
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


Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
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: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Loading required package: GenomicAlignments
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RIPSeeker/binCount.Rd_%03d_medium.png", width=480, height=480)
> ### Name: binCount
> ### Title: Count reads in nonoverlapping bins across a chromosome
> ### Aliases: binCount
> 
> ### ** Examples
> 
> # Retrieve system files
> extdata.dir <- system.file("extdata", package="RIPSeeker") 
> 
> bamFiles <- list.files(extdata.dir, ".bam$", recursive=TRUE, full.names=TRUE)
> 
> bamFiles <- grep("PRC2", bamFiles, value=TRUE)
> 
> alignGal <- getAlignGal(bamFiles[1], reverseComplement=TRUE, genomeBuild="mm9")
Processing /home/ddbj/local/lib64/R/library/RIPSeeker/extdata/PRC2/SRR039210_processed_tophat/accepted_hits_noDup_sel_chrX.bam ... All hits are returned with flags.
> 
> alignGR <- as(alignGal, "GRanges")
> 
> alignGRList <- GRangesList(as.list(split(alignGR, seqnames(alignGR))))
> 
> binSize <- 1000
> 
> binGR <- binCount(alignGRList$chrX, binSize)
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>