readCircs: read a tabular circRNA candidate list

In BIMSBbioinfo/ciRcus: Annotation, analysis and visualization of circRNA data

Description

readCircs loads a list of circRNA candidates into a data.table. Currently supported input formats are find_circ.py and find_circ2.py.

Usage

readCircs(file, subs = "all", qualfilter = TRUE, keepCols = 1:6, ...)

Arguments

file	Input file location, a character string such as /home/user/my_circRNA_project/circ_splice_sites.bed
subs	A character string, keep only lines containing it in the name column.
qualfilter	should quality filtering be performed?
keepCols	An integer vector. Which input columns should be returned?
...	other arguments

Details

Not intended to be used directly, but will stay exported for the time being. If find_circ2.py is used, fifth column will be renamed to n_reads (from n_frags or counts, depending on the find_circ2 release) for backwards compatibility and old time's sake. Will rename "lin" to "norm" in find_circ2 input name column for the same reason. Expects <myproject>/fc2/circ_splice_sites.bed as input, and assumes the existence of <myproject>/fc2/lin_splice_sites.bed.

Value

A data table.

BIMSBbioinfo/ciRcus documentation built on May 5, 2019, 10:25 a.m.