readBam: Custom bam reader

In JokingHero/ORFik: Open Reading Frames in Genomics

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 "score" with the counts of duplicates per read. Only works for single end reads, as perfect duplication events for paired end is more rare and therefor not supported!.

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, , a seqlevelsStyle or Seqinfo. (Default: NULL) to get seqlevelsStyle from. In addition if it is a Seqinfo object, seqinfo will be updated. Example of seqlevelsStyle update: 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.bigWig(), export.fstwig(), export.wiggle(), fimport(), findFa(), fread.bed(), optimizeReads(), readBigWig(), readWig()

Examples

bam_file <- system.file("extdata/Danio_rerio_sample", "ribo-seq.bam", package = "ORFik")
readBam(bam_file, "UCSC")

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.