RUBIC

RUBIC detects recurrent copy number alterations using copy number breaks.

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:
        "0.72.0/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-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

Input/Output

Input:

  • seg
  • markers

Output:

  • out_gains
  • out_losses
  • out_plots

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"]])