readBamGappedAlignments {Rsamtools} | R Documentation |
Read a BAM file as a GappedAlignments or GappedReads object.
readBamGappedAlignments(file, index=file, use.names=FALSE, param=NULL) readBamGappedReads(file, index=file, use.names=FALSE, param=NULL)
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 |
|
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.
A GappedAlignments object for
readBamGappedAlignments
.
A GappedReads object for readBamGappedReads
.
BAM records corresponding to unmapped reads or to reads that are PCR or optical duplicates are always ignored.
H. Pages
GappedAlignments-class,
GappedReads-class,
scanBam
,
ScanBamParam
## 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))