CNV detection in mRNA , SNP array using R

Question

[Begali]

Dear all;

kindly I would like to receive about any hints for R pacakge or tutorial in order to be able to detect germline copy number variation in mRNA data as well as in SNP array... Moreover, I have only one type of sample, file for each patient related to healthy tissue in different format ( fastqc as well as Bam for mRNA) and SNP array file..

with best regards

[Kevin Blighe]

There is a thread here for CNV detection from RNA-seq: Detecting copy number alterations based on RNA-seq data

There is also CNVkit-RNA

For the SNP array, which array do you have (Affymetrix, Agilent, ...)?