R: Reading GappedAlignments or GappedReads objects from a BAM...

readBamGappedAlignments {Rsamtools}

R Documentation

Reading GappedAlignments or GappedReads objects from a BAM file

Description

Read a BAM file as a GappedAlignments or GappedReads object.

Usage

readBamGappedAlignments(file, index=file, use.names=FALSE, param=NULL)
readBamGappedReads(file, index=file, use.names=FALSE, param=NULL)

Arguments

`file`	The character(1) file name of the ‘BAM’ file to be processed.
`index`	The character(1) name of the index file of the 'BAM' file being processed; this is given without the '.bai' extension.
`use.names`	Use the query template names (QNAME field) as the names of the returned object? If not (the default), then the returned object has no names.
`param`	`NULL` or an instance of `ScanBamParam`. Like for `scanBam`, this influences what fields and which records are imported. However, please note that the fields specified thru this `ScanBamParam` object will be loaded in addition to any field required for generating the returned object (GappedAlignments or GappedReads object) and will be stored in its elementMetadata part. By default (i.e. `param=NULL`), no additional field is loaded and the flag used is `scanBamFlag(isUnmappedQuery=FALSE, isDuplicate=FALSE)` (i.e. all the records corresponding to mapped reads that are not PCR or optical duplicates are loaded).

Details

See ?GappedAlignments-class for a description of GappedAlignments objects.

See ?GappedReads-class for a description of GappedReads objects.

See ?scanBam for a description of the arguments.

Value

A GappedAlignments object for readBamGappedAlignments.

A GappedReads object for readBamGappedReads.

Note

BAM records corresponding to unmapped reads or to reads that are PCR or optical duplicates are always ignored.

Author(s)

H. Pages

Examples

## Simple use:
bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools")
galn1 <- readBamGappedAlignments(bamfile)
galn1
names(galn1)

## Using the 'use.names' arg:
galn2 <- readBamGappedAlignments(bamfile, use.names=TRUE)
galn2
head(names(galn2))

## Using the 'param' arg to load additional BAM fields:
param <- ScanBamParam(what=c("qual", "flag"))
galn3 <- readBamGappedAlignments(bamfile, param=param)
galn3
elementMetadata(galn3)

## Using the 'param' arg to load reads from particular regions.
## Note that if we weren't providing a 'what' argument here, all the
## BAM fields would be loaded:
which <- RangesList(seq1=IRanges(1000, 2000),
                    seq2=IRanges(c(100, 1000), c(1000, 2000)))
param <- ScanBamParam(which=which)
galn4 <- readBamGappedAlignments(bamfile, param=param)
galn4

## Note that a given record is loaded one time for each region it
## belongs to (this is a scanBam() feature, readBamGappedAlignments()
## is based on scanBam()):
which <- IRangesList(seq2=IRanges(c(1563, 1567), width=1))
param <- ScanBamParam(which=which)
galn5 <- readBamGappedAlignments(bamfile, param=param)
galn5

## Using the 'param' arg to load tags. Except for MF and Aq, the tags
## specified below are predefined tags (see the SAM Spec for the list
## of predefined tags and their meaning).
param <- ScanBamParam(tag=c("MF", "Aq", "NM", "UQ", "H0", "H1"),
                      what="isize")
galn6 <- readBamGappedAlignments(bamfile, param=param)
elementMetadata(galn6)  # "tag" cols always after "what" cols

## readBamGappedReads():
greads1 <- readBamGappedReads(bamfile)
greads1
names(greads1)
qseq(greads1)
greads2 <- readBamGappedReads(bamfile, use.names=TRUE)
greads2
head(names(greads2))

[Package Rsamtools version 1.6.3 Index]