oncosnp: A function to handle a docker containier executing CNV...

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

A function to handle a docker containier executing CNV calculation. Only supporting hg19

Description

This function executes a ubuntu docker that produces as output oncosnp and request as input a tabl delimited file with Name Chromosome Position Log R Ratio B Allele Freq, where Name is the snp id from Illumina arrays, Chromosome is the chr, POsition is the SNP location in the chr Log R Ratio B Allele Freq are genrated from genomestudio

Usage

oncosnp(
  group = c("sudo", "docker"),
  data.folder,
  scratch.folder,
  sample.name = NULL,
  blood.name = NULL
)

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 are located and where output will be written
scratch.folder	a character string indicating the scratch folder for temporary operations
sample.name	a character string indicating snp data file name
blood.name	a character string indicating snp data file name for blood snp

Value

cnv1.cnvs, cnv2,cnvs and other oncosnp elements, see oncosnp help page for further information

Author(s)

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

Examples

## Not run: 
    system("wget http://130.192.119.59/public/testcnv.zip")
    #running fastqc
    oncosnp(group="docker", data.folder=getwd(), scratch.folder="/data/scratch", sample.name="sampleXX.txt", blood.name=NULL)

## End(Not run)

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