RUBIC¶
RUBIC detects recurrent copy number alterations using copy number breaks.
Software dependencies¶
- r-base =3.4.1
- r-rubic =1.0.3
- r-data.table =1.10.4
- r-pracma =2.0.4
- r-ggplot2 =2.2.1
- r-gtable =0.2.0
- r-codetools =0.2_15
- r-digest =0.6.12
Example¶
This wrapper can be used in the following way:
rule rubic:
input:
seg="{samples}/segments.txt",
markers="{samples}/markers.txt"
output:
out_gains="{samples}/gains.txt",
out_losses="{samples}/losses.txt",
out_plots=directory("{samples}/plots") #only possible to provide output directory for plots
params:
fdr="",
genefile=""
wrapper:
"0.32.0/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.
Authors¶
- Beatrice F. Tan
Code¶
# __author__ = "Beatrice F. Tan"
# __copyright__ = "Copyright 2018, Beatrice F. Tan"
# __email__ = "beatrice.ftan@gmail.com"
# __license__ = "LUMC"
library(RUBIC)
all_genes <- if (snakemake@params[["genefile"]] == "") system.file("extdata", "genes.tsv", package="RUBIC") else snakemake@params[["genefile"]]
fdr <- if (snakemake@params[["fdr"]] == "") 0.25 else snakemake@params[["fdr"]]
rbc <- rubic(fdr, snakemake@input[["seg"]], 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"]])