oncosnpAnnotation: A function to associate CNV generated by oncSNP starting from...

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

A function to associate CNV generated by oncSNP starting from log R ratio and B allel frequences, generated by SNP arrays, to gene symbols

Description

This function executes a ubuntu docker that uses as input the cnvs files produced by oncoSNP and add CN and LOH (check oncoSNP readme for more info) fields (rank 5 only) to the genes characterized by having genomics cohordinates included in the CNV region

Usage

oncosnpAnnotation(group = c("sudo", "docker"), data.folder, genome.folder)

Arguments

group	a character string. Two options: sudo or docker, depending to which group the user belongs
data.folder	a character string indicating the folder where input data (.cnvs) generated with oncoSNP are located and where output will be written
genome.folder	a character string indicating the path of the folder where ENSEMBL genome.gtf is located, IMPORTANT use the same genome assembly used to design the array.

Value

a file for each .cnvs, e.g. annotation_XXXX.cnvs.txt

Author(s)

Raffaele Calogero, raffaele.calogero[at]unito[dot]it, University of Torino, Italy

Examples

## Not run: 
    #running oncosnpAnnotation
system("wget http://130.192.119.59/public/test_oncosnp.zip")
system("unzip test_oncosnp.zip")
oncosnpAnnotation(group="docker", data.folder="./test_oncosnp/oncosnp_out", genome.folder="./test_oncosnp/hg19")

## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.