Combine alignment files into a single GAlignments object

Description

Import and process individual BAM/SAM/BED alignment files using getAlignGal and combine them into a single GAlignments.

Usage

combineAlignGals(bamFiles, ...)

Arguments

Details

If there is only one BAM file, then simply return the output from getAlignGal; otherwise, all processed alignments are pooled to form a single GAlignments object.

Value

.

Note

User are recommanded to pool technical replicates but keep biological replicate separate for confirmation.

Author(s)

Yue Li

See Also

getAlignGal, readGAlignments, readGAlignmentPairs, import

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)

# combine the alignments for technical replicates
alignGal <- 
combineAlignGals(bamFiles=grep(pattern="SRR039214", 
                  bamFiles, value=TRUE, invert=TRUE), 
                  reverseComplement=TRUE, genomeBuild="mm9")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Type 'demo()' for some demos, 'help()' for on-line help, or
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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/combineAlignGals.Rd_%03d_medium.png", width=480, height=480)
> ### Name: combineAlignGals
> ### Title: Combine alignment files into a single GAlignments object
> ### Aliases: combineAlignGals
> 
> ### ** 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)
> 
> # combine the alignments for technical replicates
> alignGal <- 
+ combineAlignGals(bamFiles=grep(pattern="SRR039214", 
+                   bamFiles, value=TRUE, invert=TRUE), 
+                   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.
Processing /home/ddbj/local/lib64/R/library/RIPSeeker/extdata/PRC2/SRR039211_processed_tophat/accepted_hits_noDup_sel_chrX.bam ... All hits are returned with flags.
2 BAM files are combined
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>