Description Usage Arguments Value
Takes a VCF files and reads it into VariantAnnotation package to overlap with GRanges probeset dataset of snp6.dat. It willc onvert the 0/0, 0/1, etc.. genotypes to 0,1,2. Finally, it will reutnr the BAFs and normalized BAFs for each of the overlapping probesets.
1 | mapVcf2Affy(vcfFile, snp6.dat)
|
vcfFile |
Absolute path to VCF file |
snp6.dat |
SNP6 probeset genomic position, accessible from CCLid::ccl_table |
List composed of two dataframes, BAF and GT
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