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Last data update: 2014.03.03

R: Views into a set of BAM files

BamViews

R Documentation

Views into a set of BAM files

Description

Use BamViews() to reference a set of disk-based BAM files to be processed (e.g., queried using scanBam) as a single ‘experiment’.

Usage


## Constructor
BamViews(bamPaths=character(0),
     bamIndicies=bamPaths,
     bamSamples=DataFrame(row.names=make.unique(basename(bamPaths))),
     bamRanges, bamExperiment = list(), ...)
## S4 method for signature 'missing'
BamViews(bamPaths=character(0),
     bamIndicies=bamPaths,
     bamSamples=DataFrame(row.names=make.unique(basename(bamPaths))),
     bamRanges, bamExperiment = list(), ..., auto.range=FALSE)
## Accessors
bamPaths(x)
bamSamples(x)
bamSamples(x) <- value
bamRanges(x)
bamRanges(x) <- value
bamExperiment(x)

## S4 method for signature 'BamViews'
names(x)
## S4 replacement method for signature 'BamViews'
names(x) <- value
## S4 method for signature 'BamViews'
dimnames(x)
## S4 replacement method for signature 'BamViews,ANY'
dimnames(x) <- value

bamDirname(x, ...) <- value

## Subset
## S4 method for signature 'BamViews,ANY,ANY'
x[i, j, ..., drop=TRUE]
## S4 method for signature 'BamViews,ANY,missing'
x[i, j, ..., drop=TRUE]
## S4 method for signature 'BamViews,missing,ANY'
x[i, j, ..., drop=TRUE]

## Input
## S4 method for signature 'BamViews'
scanBam(file, index = file, ..., param = ScanBamParam(what=scanBamWhat()))
## S4 method for signature 'BamViews'
countBam(file, index = file, ..., param = ScanBamParam())

## Show
## S4 method for signature 'BamViews'
show(object)

Arguments

`bamPaths`	A character() vector of BAM path names.
`bamIndicies`	A character() vector of BAM index file path names, without the ‘.bai’ extension.
`bamSamples`	A `DataFrame` instance with as many rows as `length(bamPaths)`, containing sample information associated with each path.
`bamRanges`	Missing or a `GRanges` instance with ranges defined on the reference chromosomes of the BAM files. Ranges are not validated against the BAM files.
`bamExperiment`	A list() containing additional information about the experiment.
`auto.range`	If `TRUE` and all `bamPaths` exist, populate the ranges with the union of ranges returned in the `target` element of `scanBamHeader`.
`...`	Additional arguments.
`x`	An instance of `BamViews`.
`object`	An instance of `BamViews`.
`value`	An object of appropriate type to replace content.
`i`	During subsetting, a logical or numeric index into `bamRanges`.
`j`	During subsetting, a logical or numeric index into `bamSamples` and `bamPaths`.
`drop`	A logical(1), ignored by all `BamViews` subsetting methods.

`file`	An instance of `BamViews`.
`index`	A character vector of indices, corresponding to the `bamPaths(file)`.
`param`	An optional `ScanBamParam` instance to further influence scanning or counting.

Objects from the Class

Objects are created by calls of the form BamViews().

Slots

bamPaths: A character() vector of BAM path names.
bamIndicies: A character() vector of BAM index path names.
bamSamples: A DataFrame instance with as many rows as length(bamPaths), containing sample information associated with each path.
bamRanges: A GRanges instance with ranges defined on the spaces of the BAM files. Ranges are not validated against the BAM files.
bamExperiment: A list() containing additional information about the experiment.

Functions and methods

See 'Usage' for details on invocation.

Constructor:

BamViews:: Returns a BamViews object.

Accessors:

bamPaths: Returns a character() vector of BAM path names.
bamIndicies: Returns a character() vector of BAM index path names.
bamSamples: Returns a DataFrame instance with as many rows as length(bamPaths), containing sample information associated with each path.
bamSamples<-: Assign a DataFrame instance with as many rows as length(bamPaths), containing sample information associated with each path.
bamRanges: Returns a GRanges instance with ranges defined on the spaces of the BAM files. Ranges are not validated against the BAM files.
bamRanges<-: Assign a GRanges instance with ranges defined on the spaces of the BAM files. Ranges are not validated against the BAM files.
bamExperiment: Returns a list() containing additional information about the experiment.
names: Return the column names of the BamViews instance; same as names(bamSamples(x)).
names<-: Assign the column names of the BamViews instance.
dimnames: Return the row and column names of the BamViews instance.
dimnames<-: Assign the row and column names of the BamViews instance.

Methods:

"[": Subset the object by bamRanges or bamSamples.
scanBam: Visit each path in bamPaths(file), returning the result of scanBam applied to the specified path. bamRanges(file) takes precedence over bamWhich(param).
countBam: Visit each path in bamPaths(file), returning the result of countBam applied to the specified path. bamRanges(file) takes precedence over bamWhich(param).
show: Compactly display the object.

Author(s)

Martin Morgan

Examples

fls <- system.file("extdata", "ex1.bam", package="Rsamtools",
                   mustWork=TRUE)
rngs <- GRanges(seqnames = Rle(c("chr1", "chr2"), c(9, 9)),
                ranges = c(IRanges(seq(10000, 90000, 10000), width=500),
                           IRanges(seq(100000, 900000, 100000), width=5000)),
                Count = seq_len(18L))
v <- BamViews(fls, bamRanges=rngs)
v
v[1:5,]
bamRanges(v[c(1:5, 11:15),])
bamDirname(v) <- getwd()
v

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Rsamtools)
Loading required package: GenomeInfoDb
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

Loading required package: S4Vectors

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: Biostrings
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Rsamtools/BamViews-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: BamViews
> ### Title: Views into a set of BAM files
> ### Aliases: BamViews-class BamViews BamViews,missing-method
> ###   BamViews,GRanges-method bamPaths bamIndicies bamSamples bamRanges
> ###   bamExperiment bamDirname<- bamSamples<- bamRanges<-
> ###   names,BamViews-method names<-,BamViews-method dim,BamViews-method
> ###   dimnames,BamViews-method dimnames<-,BamViews-method
> ###   dimnames<-,BamViews,ANY-method [,BamViews,ANY,missing-method
> ###   [,BamViews,missing,ANY-method [,BamViews,ANY,ANY-method
> ###   [,BamViews,ANY,missing-method scanBam,BamViews-method
> ###   countBam,BamViews-method show,BamViews-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> fls <- system.file("extdata", "ex1.bam", package="Rsamtools",
+                    mustWork=TRUE)
> rngs <- GRanges(seqnames = Rle(c("chr1", "chr2"), c(9, 9)),
+                 ranges = c(IRanges(seq(10000, 90000, 10000), width=500),
+                            IRanges(seq(100000, 900000, 100000), width=5000)),
+                 Count = seq_len(18L))
> v <- BamViews(fls, bamRanges=rngs)
> v
BamViews dim: 18 ranges x 1 samples 
names: ex1.bam 
detail: use bamPaths(), bamSamples(), bamRanges(), ... 
> v[1:5,]
BamViews dim: 5 ranges x 1 samples 
names: ex1.bam 
detail: use bamPaths(), bamSamples(), bamRanges(), ... 
> bamRanges(v[c(1:5, 11:15),])
GRanges object with 10 ranges and 1 metadata column:
       seqnames           ranges strand |     Count
          <Rle>        <IRanges>  <Rle> | <integer>
   [1]     chr1 [ 10000,  10499]      * |         1
   [2]     chr1 [ 20000,  20499]      * |         2
   [3]     chr1 [ 30000,  30499]      * |         3
   [4]     chr1 [ 40000,  40499]      * |         4
   [5]     chr1 [ 50000,  50499]      * |         5
   [6]     chr2 [200000, 204999]      * |        11
   [7]     chr2 [300000, 304999]      * |        12
   [8]     chr2 [400000, 404999]      * |        13
   [9]     chr2 [500000, 504999]      * |        14
  [10]     chr2 [600000, 604999]      * |        15
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths
> bamDirname(v) <- getwd()
> v
BamViews dim: 18 ranges x 1 samples 
names: ex1.bam 
detail: use bamPaths(), bamSamples(), bamRanges(), ... 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>