run.bicseq.cnv.pipeline: Run the BIC-seq CNV Analysis Pipeline

In rdeborja/NGS.Tools.BICseq: BICseq CNV calling pipeline

Description

Run the BIC-seq CNV analysis pipeline and generate a segmentation file

Usage

run.bicseq.cnv.pipeline(tumour, normal, chr = get.bicseq.chr(), bin = 100, lambda = 2, winSize = 200 , quant = 0.95, mult = 1)

Arguments

tumour	BAM file from tumour sample
normal	BAM file from normal sample
chr	character vector containing name of chromosomes to review
bin	initial genomic bin size to use, default: 100
lambda	penalty of the BIC, larger lambda gives a smoother profile, default: 2
winSize	window size for outlier detection, default: 200
quant	the probability of the read count quantile, default: 0.95
mult	positive integer, see BICseq HowTo vignette for details, default: 1

Author(s)

Richard de Borja

Examples

# ensure consistent results between runs
set.seed(12345);

# create a list of potential locations for the datasets
data.directories <- paste(.libPaths(), '/NGS.Tools.BICseq', sep = '');
data.directories <- c('./', data.directories);

# look in the Rcheck directory to get dataset file
data.directories <- c(getwd(), data.directories);

# search all the locations for the normal file
file.checks <- file.exists(paste(data.directories, 'extdata/normal_sorted.bam', sep = '/'));

# check to see if the file was actually found
if (any(file.checks)) {
	data.directory <- data.directories[order(file.checks, decreasing = TRUE)[1]];
} else {
	stop('Unable to find dataset file for processing');
	}
normal <- paste(data.directory, 'extdata/normal_sorted.bam', sep = '/');

# search all the locations for the normal file
file.checks <- file.exists(paste(data.directories, 'extdata/tumor_sorted.bam', sep = '/'));

# check to see if the file was actually found
if (any(file.checks)) {
	data.directory <- data.directories[order(file.checks, decreasing = TRUE)[1]];
} else {
	stop('Unable to find dataset file for processing');
	}
tumour <- paste(data.directory, 'extdata/tumor_sorted.bam', sep = '/');

bicseq <- run.bicseq.cnv.pipeline(
	normal = normal,
	tumour = tumour,
	chr = c('chr22')
	);

rdeborja/NGS.Tools.BICseq documentation built on May 27, 2019, 3:05 a.m.