fimport: Load any type of sequencing reads

In JokingHero/ORFik: Open Reading Frames in Genomics

Load any type of sequencing reads

Description

Wraps around ORFik file format loaders and rtracklayer::import and tries to speed up loading with the use of data.table. Supports gzip, gz, bgz compression formats. Also safer chromosome naming with the argument chrStyle

Usage

fimport(path, chrStyle = NULL, param = NULL, strandMode = 0)

Arguments

path	a character path to file (1 or 2 files), or data.table with 2 colums(forward&reverse) or a GRanges/Galignment/GAlignmentPairs object etc. If it is ranged object it will presume to be already loaded, so will return the object as it is, updating the seqlevelsStyle if given.
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

NOTE: For wig/bigWig files you can send in 2 files, so that it automatically merges forward and reverse stranded objects. You can also just send 1 wig/bigWig file, it will then have "*" as strand.

Value

a GAlignments/GRanges object, depending on input.

See Also

Other utils: bedToGR(), convertToOneBasedRanges(), export.bed12(), export.bigWig(), export.fstwig(), export.wiggle(), findFa(), fread.bed(), optimizeReads(), readBam(), readBigWig(), readWig()

Examples

bam_file <- system.file("extdata/Danio_rerio_sample", "ribo-seq.bam", package = "ORFik")
fimport(bam_file)
# Certain chromosome naming
fimport(bam_file, "NCBI")
# Paired end bam strandMode 1:
fimport(bam_file, strandMode = 1)
# (will have no effect in this case, since it is not paired end)

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