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

Description Usage Arguments

View source: R/file_io.R

Description

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

Usage

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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 July 3, 2020, 9:57 a.m.