tx_reads: Transcriptomic reads convertion

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

Transcriptomic reads convertion

Description

Assign aligned reads to their respective gene models and convert their positions into their corresponding transcriptomic coordinate system. It also stitches together paired-end aligned reads into a single sequence in which dots '.' separate Read1 and Read2 by their corresponding insert.

Usage

tx_reads(
  reads,
  geneAnnot,
  minReads = 50,
  withSeq = FALSE,
  verbose = TRUE,
  ignore.strand = FALSE,
  nCores = 1
)

Arguments

reads	GAlignments or GAlignmentPairs. Genomic alignments to be processed
geneAnnot	GRanges. Gene annotation as loaded by tx_load_bed()
minReads	integer. Minimum number of alignments required to overlap a gene
withSeq	logical. Set to TRUE if sequence should be preserved; 'reads' object should contain sequences.
verbose	logical. Set to FALSE to show less information.
ignore.strand	logical. Set to TRUE to allow alignments in a gene ignoring the strand of the alignment. False by default.
nCores	integer. Number of cores to run the function with. Multi-core capability not available in Windows OS.

Details

To retrieve unassigned alignments use the function tx_get_unassignedAlignments()

Value

GRanges

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