FilterChimeric_Ularcirc: Wrapper function for Ularcirc shiny app which expects a list...

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

Wrapper function for Ularcirc shiny app which expects a list of objects to be returned

Description

NEED to ensure that unstranded boolean value is passed to this function Not tested via shiny app yet.

Usage

FilterChimeric_Ularcirc(
  All_junctions,
  chromFilter = TRUE,
  strandFilter = TRUE,
  genomicDistance = c(200, 1e+05),
  canonicalJuncs = TRUE,
  fileID = c(-1),
  chrM_Filter = TRUE,
  invertReads = FALSE,
  unstranded = FALSE,
  summaryNumber = 50
)

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).
unstranded	: Boolen for if reads are unstranded
summaryNumber	: Number (Integer) of records to display in shiny app

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