tx_load_bam: Read paired end bam file by yield size

In AngelCampos/txtools: An R package facilitating analysis of RNA modifications, structures, and interactions

Read paired end bam file by yield size

Description

Reads a file in BAM format by blocks of lines equal to a yield size, either automatically calculated or specified by the user, and loads it as a GenomicAlignments object.

Usage

tx_load_bam(
  file,
  pairedEnd,
  yieldSize = 1e+05,
  scanFlag = "default",
  loadSeq = FALSE,
  strandMode = 1,
  loadSecondaryAligns = NA,
  verbose = TRUE
)

Arguments

file	character. Path to the file to read
pairedEnd	logical. Set to FALSE if reads in BAM file are single-end, set to TRUE if reads are paired-end.
yieldSize	numeric. Number of reads to be processed at a time
scanFlag	integer. Flag used to filter reads. Built with the scanBamFlag function.
loadSeq	logical. Set to TRUE for loading the sequences contained in the BAM file
strandMode	numeric. 1 (default): Strand of the pair is that of its first alignment: Directional Illumina (Ligation), Standard SOLiD. (Single-end No change in strand) 2: strand of the pair is strand of its last alignment: dUTP, NSR, NNSR, Illumina stranded TruSeq PE protocol. (Single-end: Change to inverse strand) 0: strand of the pair is set to '*' (unspecified). This mode is no longer supported by tx_reads() . More info: GAlignmentPairs-class.
loadSecondaryAligns	logical. Set to FALSE to discard alignments labeled in the BAM file as secondary and load only primary alignments, set to TRUE to load only secondary alignments, leave as NA to load both primary and secondary alignments.
verbose	logical. Set to FALSE to show less information.

Value

GRanges

Examples

# Loading in-package BAM file
bamFile <- system.file("extdata", "example_hg19.bam", package = "txtools")
hg19_bam <- tx_load_bam(bamFile, pairedEnd = TRUE, loadSeq = TRUE, verbose = TRUE)
summary(hg19_bam)

AngelCampos/txtools documentation built on Sept. 16, 2024, 10:25 p.m.