CNV detection in mRNA , SNP array using R
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
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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, ...)?