readBam {ORFik}R Documentation

Custom bam reader

Description

Safer version that handles the most important error done. In the future will use a faster .bam loader for big .bam files in R.

Usage

readBam(path, chrStyle = NULL)

Arguments

path

a character path to .bam file. If paired end bam files, input must be a data.table with two columns (forward and reverse) and one row:
if paired end reads in single bam file:
forward contains paired end bam file path, reverse must be either "paired-end" or "" (single end).
if paired end reads split in two files:
forward contains paired end bam file path (R1), reverse must be paired end bam file path (R2 file), this is a rare case
If all are single-end or you don't need to load data as paired end, the reverse column can be skipped.

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"

Value

a GAlignments 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 1.8.6 Index]