Rawcopy is an R package for processing of Affymetrix CytoScan HD, CytoScan 750k and SNP 6.0 microarrays for copy number analysis. It takes CEL files (raw microarray intensity values) as input. Output consists of:

Log ratio: normalized intensity per probe relative to sample median and a reference data set

B-allele frequency or BAF: estimated abundance of the B allele relative to total abundance, SNP probes only

Segments: genomic segments of unchanging copy number, estimated using the PSCBS package

Figures: several figures per sample and sample set are plotted for the user's convenience, some examples are shown below