RUBIC
RUBIC detects recurrent copy number alterations using copy number breaks.
URL: https://github.com/NKI-CCB/RUBIC
Example
This wrapper can be used in the following way:
rule rubic:
input:
seg="{samples}/segments.txt",
markers="{samples}/markers.txt"
# genefile="path/to/genefile"
output:
out_gains="out/{samples}/gains.txt",
out_losses="out/{samples}/losses.txt",
out_plots=directory("out/{samples}/plots") #only possible to provide output directory for plots
log:
"logs/{samples}/rubic.log"
params:
fdr=0.2,
wrapper:
"v5.7.0/bio/rubic"
Note that input, output and log file paths can be chosen freely.
When running with
snakemake --use-conda
the software dependencies will be automatically deployed into an isolated environment before execution.
Software dependencies
r-rubic=1.0.3
libgfortran=3.0.0
r-data.table=1.11.4
Input/Output
Input:
seg
markers
genefile
Output:
out_gains
out_losses
out_plots
Params
fdr
: false discovery rate (optional, leave empty to use default value of 0.25)
Code
# __author__ = "Beatrice F. Tan"
# __copyright__ = "Copyright 2018, Beatrice F. Tan"
# __email__ = "beatrice.ftan@gmail.com"
# __license__ = "LUMC"
library(RUBIC)
all_genes <- if ("genefile" %in% snakemake@input) snakemake@input[["genefile"]] else system.file("extdata", "genes.tsv", package="RUBIC")
fdr <- if ("fdr" %in% snakemake@params) snakemake@params[["fdr"]] else 0.25
rbc <- rubic(fdr=fdr, seg.cna=snakemake@input[["seg"]], markers=snakemake@input[["markers"]], genes=all_genes)
rbc$save.focal.gains(snakemake@output[["out_gains"]])
rbc$save.focal.losses(snakemake@output[["out_losses"]])
rbc$save.plots(snakemake@output[["out_plots"]])