Commit 125ef5d2 authored by Beatrice Tan's avatar Beatrice Tan

Removed scripts which are not used.

parent c339d65e
#Directories to be specified
#workdir: /home/bftan/CNA_results #directory to write output
#gisticdir: /home/bftan/Tools/GISTIC2_test #directory to install GISTIC2
#workdir: /home/bftan/CNA_results #directory to write output
#gisticdir: /home/bftan/Tools/GISTIC2 #directory to install GISTIC2
workdir: /home/beatrice/CNA_analysis
gisticdir: /home/beatrice/CNA_analysis/run_gistic2
#Input details to download from firehose
cancer_type: SKCM
date_data: "2016_07_15"
#Or provide input file
inputfile: "" #tumor segmentation data
normal: "" #normal segmentation data
#Data for running and benchmarking tools.
reference: hg19
prev_found_genes: input_files/intogen-CM-drivers-data.tsv
census_genes: input_files/Census_genes.txt
biomart_genes: input_files/biomart_human_genes.tsv
#Settings GISTIC2.0
gistic_precision: "99"
settings_gistic: "-ta 0.1
-td 0.1
-qvt 0.25
-brlen 0.7
-cap 1.5
-rx 1
-genegistic 1
-conf 0.99"
#Settings for sample size differences
sizes: [20, 30, 40, 50, 60, 70, 80, 90]
#sizes: [30, 40]
repeats: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]
#!/usr/bin/env Rscript
args = commandArgs(trailingOnly=TRUE)
source("https://bioconductor.org/biocLite.R")
biocLite("karyoploteR")
bed = read.table(args[1], sep="\t", header=TRUE)
#Read output plot files?
#chrom as "chr1"
kp <- plotKaryotype(chromosomes=c(chrom))
#kpDataBackground(kp)
kpAxis(kp)
kpRect(kp, chr=chrom, x0=start, x1=end, y0=0.2, y1=0.4)
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