FilterChimericJuncs: FilterChimericJuncs

In VCCRI/Ularcirc: Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)

FilterChimericJuncs

Description

A generic function that filters STAR chimeric junction files on certain genomic criteria (eg strand, same chromosome etc). Useful filter to remove the most obvious false positives. The default filter settings are suitable for circRNA discovery in humans / mice data sets.

Usage

FilterChimericJuncs(
  All_junctions,
  chromFilter = TRUE,
  strandFilter = TRUE,
  genomicDistance = c(200, 1e+05),
  canonicalJuncs = TRUE,
  fileID = c(-1),
  chrM_Filter = TRUE,
  invertReads = FALSE
)

Arguments

All_junctions	: data.table of chimeric reads from STAR aligner
chromFilter	: when TRUE (default) both chimera parts have to align to same chromosome
strandFilter	: when TRUE (default) both chimera parts have to align to same strand
genomicDistance	: minimum and maximum distance filters of chimeric reads on chromosome. Only is applied if ChromFilter is TRUE and StrandFilter is TRUE
canonicalJuncs	: Will include any canonical junctions (default TRUE). Note STAR keeps canonical junctions that do not conform to aligner rules.
fileID	: Specify a file index. Useful if planing to concatenating all data sets into a single table.
chrM_Filter	: Filter out mitochondrial chimeric reads (default TRUE)
invertReads	: Boolean that specifies in read strand should be inverted (default FALSE).

See Also

SelectUniqueJunctions, loadSTAR_chimeric

Examples

extdata_path <- system.file("extdata",package = "Ularcirc")
chimeric.file <- paste0(extdata_path,"/SRR444655_subset.Chimeric.out.junction.gz")
chimericsDT <- Ularcirc::loadSTAR_chimeric(chimeric.file,returnColIdx = 1:14)
chimericsDT$filtered <- Ularcirc::FilterChimericJuncs(chimericsDT$data_set, canonicalJuncs = TRUE)

VCCRI/Ularcirc documentation built on April 8, 2022, 5:17 p.m.