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:
        "v4.6.0/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

Params

• fdr: false discovery rate (optional, leave empty to use default value of 0.25)

• genefile: file path to use custom gene file (optional, leave empty to use default file)

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"]])