mapVcf2Affy: mapVcf2Affy
In quevedor2/CCLid: Compares Cancer Cell Line Genotypes Against Pharmacogenomic Datasets
Description
Usage
Arguments
Value
Description
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.
Usage
1
mapVcf2Affy(vcfFile, snp6.dat)
Arguments
vcfFile
Absolute path to VCF file
snp6.dat
SNP6 probeset genomic position, accessible from CCLid::ccl_table
Value
List composed of two dataframes, BAF and GT
quevedor2/CCLid documentation built on July 15, 2020, 4:05 a.m.
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Description Usage Arguments Value
Description
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.
Usage
1 | mapVcf2Affy(vcfFile, snp6.dat)
|
Arguments
vcfFile |
Absolute path to VCF file |
snp6.dat |
SNP6 probeset genomic position, accessible from CCLid::ccl_table |
Value
List composed of two dataframes, BAF and GT
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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