writeAbraSv: Write an abra.sv file

In jefferys/FusionClust: Cluster fusions

Description

Write 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

writeAbraSv(fusions, file, stranded = FALSE)

Arguments

fusions	The file Can be a single abra sv file, or a merged file with results for multuple samples.
file	The abra.sv fusion data file to write.

Value

A data frame object 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.