fimport {ORFik} | R Documentation |
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
fimport(path, chrStyle = NULL, param = NULL, strandMode = 0)
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,
or a |
param |
By default (i.e. |
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. |
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.
a GAlignments
/GRanges
object,
depending on input.
Other utils:
bedToGR()
,
convertToOneBasedRanges()
,
export.bed12()
,
export.bigWig()
,
export.wiggle()
,
findFa()
,
fread.bed()
,
optimizeReads()
,
readBam()
,
readBigWig()
,
readWig()
bam_file <- system.file("extdata", "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)