readBam {ORFik} | R Documentation |
Custom bam reader
Description
Read in Bam file from either single end or paired end.
Safer combined version of readGAlignments
and
readGAlignmentPairs that takes care of some common errors.
If QNAMES of the aligned reads are from collapsed fasta files
(if the names are formated from collapsing in either
(ORFik, ribotoolkit or fastx)), the
bam file will contain a meta column called collapsed with the counts
of duplicates per read.
Usage
readBam(path, chrStyle = NULL, param = NULL, strandMode = 0)
Arguments
path |
a character / data.table with path to .bam file. There
are 3 input file possibilities.
single end : a character path (length 1)
paired end (1 file) : Either a character path (length of 2), where
path[2] is "paired-end", or a data.table
with 2 columns, forward = path & reverse = "paired-end"
paired end (2 files) : Either a character path (length of 2), where
path[2] is path to R2, or a data.table
with 2 columns, forward = path to R1 & reverse = path to R2.
(This one is not used often)
|
chrStyle |
a GRanges object, TxDb, FaFile,
or a seqlevelsStyle
(Default: NULL) to get seqlevelsStyle from. Is chromosome 1
called chr1 or 1, is mitocondrial chromosome called MT or chrM etc.
Will use 1st seqlevel-style if more are present.
Like: c("NCBI", "UCSC") -> pick "NCBI"
|
param |
NULL or a ScanBamParam object.
Like for scanBam , this influences what fields
and which records are imported. However, note that the fields specified
thru this ScanBamParam object will be loaded
in addition to any field required for generating the returned
object (GAlignments, GAlignmentPairs,
or GappedReads object),
but only the fields requested by the user will actually be kept as
metadata columns of the object.
By default (i.e. param=NULL or param=ScanBamParam() ), no
additional field is loaded. The flag used is
scanBamFlag(isUnmappedQuery=FALSE) for
readGAlignments , readGAlignmentsList , and
readGappedReads .
(i.e. only records corresponding to mapped reads are loaded),
and scanBamFlag(isUnmappedQuery=FALSE, isPaired=TRUE,
hasUnmappedMate=FALSE) for readGAlignmentPairs
(i.e. only records corresponding to paired-end reads with both ends
mapped are loaded).
|
strandMode |
numeric, default 0. Only used for paired end bam files.
One of (0: strand = *, 1: first read of pair is +, 2: first read of pair is -).
See ?strandMode. Note: Sets default to 0 instead of 1, as readGAlignmentPairs uses 1.
This is to guarantee hits, but will also make mismatches of overlapping
transcripts in opposite directions.
|
Details
In the future will use a faster .bam loader for big .bam files in R.
Value
a GAlignments
or GAlignmentPairs
object of bam file
See Also
Other utils:
bedToGR()
,
convertToOneBasedRanges()
,
export.bed12()
,
export.wiggle()
,
fimport()
,
findFa()
,
fread.bed()
,
optimizeReads()
,
readWig()
Examples
bam_file <- system.file("extdata", "ribo-seq.bam", package = "ORFik")
readBam(bam_file, "UCSC")
[Package
ORFik version 1.10.13
Index]