Hi all,
I have MeDIP-seq data on 4 tumor samples and adjacent normal tissue. In addition, I have INPUT (sequenced non-enriched control same tissue) for each of the sample (8 MEDIPS BAM files and 8 INPUT BAM files). I was wondering whether I can use the INPUT control BAM files in addEnrichmentParameters() rather than using TCGA 450K Human Methylation Calibration Dataset?
I was wondering if anyone has any suggestions as to what R packages or software I can use to produce a similar R object using the INPUT BAM files?
Regards
Gaurav