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

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

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

Examples

if (FALSE) {
    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)
}