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,
  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. See ScanBamParam
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.
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 April 8, 2024, 6:06 p.m.