readAbraSv: Read an abra.sv file

In jefferys/FusionClust: Cluster fusions

Description

Read in a sample's abra.sv.txt file, or a merged (concatenated) abra.sv.txt file with an extra (initial) column giving the sample name.

Usage

readAbraSv(file, stranded = FALSE, orderedEnds = TRUE, tumorOnly = FALSE)

Arguments

file	The abra.sv fusion data file to load. Can be a single abra sv file, or a merged file with results for multuple samples.
stranded	Boolean indicating if the abra file has strand information. Currently, setting this TRUE will prevent processing as stradedness is not implemented. Default is FALSE.
orderedEnds	Boolean indicating if the output should order the two fusions ends canonically (ref, then pos), so the earlier one is first. Default is TRUE.
tumorOnly	Boolean indicating if the abra file has one column, e.g. tumor only or two columns of data, e.g. tumor and normal. Default is FALSE.

Value

Returns a data frame describing the fusions, with columns:

• sample [optional] The sample this fusion came from.

• group The group name (within sample) of equivalent fusions.

• chr1 End1's chromosome, parsed from <chr>:<pos>.

• pos1 End1's position, parsed from <chr>:<pos>.

• chr1 End2's chromosome, parsed from <chr>:<pos>.

• pos1 End2's position, parsed from <chr>:<pos>.

• orientation The relative directionality of end1 and end2, as blank " " if in the same direction (FF or RR from input), or as "I" if relatively inverted (FR or RF fromn input).

• normal_count The number of split reads containing the fusion point in the normal sample.

• tumor_count The number of split reads containing the fusion point in the tumor sample.

Examples

svFile <- "tests/testthat/data/perSampleAbraSv.tsv"
svFile <- system.file( svFile, package= "fusionClust" )
fusions <- loadAbraSv( svFile )

jefferys/FusionClust documentation built on May 22, 2019, 2:39 p.m.