Preparing the results of tallyBAM for writing to an HDF5 tally file

Description

This function tallies a set of bam files and prepares the data for writing to an HDF5 tally file.

Usage

applyTallies( bamfiles, chrom, start, stop, q=25, ncycles = 0, max.depth=1000000, prepForHDF5 = TRUE, reference = NULL)

Arguments

Details

This is a wrapper function for applying tallyBAM to a set of bam files specified in the bamfiles argument. If prepForHDF5 is not true the result is equivalent to calling tallyBAM with lapply on the file names, otherwise the resulting data structure has the same layout as the return value of h5readBlock and can be written to an HDF5 tally file directly. The order or samples along the sample dimension is the same as the order of the file names (i.e. the order of the bamfiles argument).

Value

A list with slots containing the Counts,Coverages,Deletions and Reference datasets for the given sample if prepForHDF5 is true, a list of 3D-arrays (Nucleotide x Strand x Position) otherwise.

Author(s)

Paul Pyl

Examples

library(h5vc)
library(BSgenome.Hsapiens.UCSC.hg19)
files <- c("NRAS.AML.bam","NRAS.Control.bam")
bamFiles <- file.path( system.file("extdata", package = "h5vcData"), files)
chrom = "1"
startpos <- 115247090
endpos <- 115259515
theData <- applyTallies( bamFiles, reference = Hsapiens[["chr1"]][startpos:endpos], chr = chrom, start = startpos, stop = endpos, ncycles = 10 )
str(theData)

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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> library(h5vc)
Loading required package: grid
Loading required package: gridExtra
Loading required package: ggplot2
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/h5vc/applyTallies.Rd_%03d_medium.png", width=480, height=480)
> ### Name: applyTallies
> ### Title: Preparing the results of tallyBAM for writing to an HDF5 tally
> ###   file
> ### Aliases: applyTallies
> 
> ### ** Examples
> 
> library(h5vc)
> library(BSgenome.Hsapiens.UCSC.hg19)
Loading required package: BSgenome
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 object is masked from 'package:gridExtra':

    combine

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: 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: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
> files <- c("NRAS.AML.bam","NRAS.Control.bam")
> bamFiles <- file.path( system.file("extdata", package = "h5vcData"), files)
> chrom = "1"
> startpos <- 115247090
> endpos <- 115259515
> theData <- applyTallies( bamFiles, reference = Hsapiens[["chr1"]][startpos:endpos], chr = chrom, start = startpos, stop = endpos, ncycles = 10 )
> str(theData)
List of 4
 $ Counts   : num [1:12, 1:2, 1, 1:2, 1:12426] 0 0 0 0 0 0 0 0 0 0 ...
  ..- attr(*, "dimnames")=List of 5
  .. ..$ : chr [1:12] "A.front" "C.front" "G.front" "T.front" ...
  .. ..$ : NULL
  .. ..$ : chr "/home/ddbj/local/lib64/R/library/h5vcData/extdata/NRAS.Control.bam"
  .. ..$ : chr [1:2] "+" "-"
  .. ..$ : NULL
 $ Coverages: num [1:2, 1, 1:2, 1:12426] 0 0 0 0 0 0 0 0 0 0 ...
  ..- attr(*, "dimnames")=List of 4
  .. ..$ : NULL
  .. ..$ : chr "/home/ddbj/local/lib64/R/library/h5vcData/extdata/NRAS.Control.bam"
  .. ..$ : chr [1:2] "+" "-"
  .. ..$ : NULL
 $ Deletions: num [1, 1:2, 1:2, 1:12426] 0 0 0 0 0 0 0 0 0 0 ...
  ..- attr(*, "dimnames")=List of 4
  .. ..$ : chr "/home/ddbj/local/lib64/R/library/h5vcData/extdata/NRAS.Control.bam"
  .. ..$ : NULL
  .. ..$ : chr [1:2] "+" "-"
  .. ..$ : NULL
 $ Reference: num [1:12426] 3 3 0 3 2 0 1 3 0 0 ...
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>