Description Usage Arguments Value
View source: R/paper_functions.R
Check the drift of a given VCF file and all matching cell line names based on the meta-data matched IDs
1 2 3 4 5 6 7 8 9 | getVcfDrifts(
vcfFile,
ref.dat,
meta.df,
min.depth = 5,
centering = "extreme",
dataset = "GDSC",
snp6.dat
)
|
vcfFile |
path to vcf file |
ref.dat |
Refrence data containing Reference matrix and variance |
meta.df |
Meta file linking RNA files to cell names |
min.depth |
Minimum depth to consider for SNPs |
centering |
Centering of data method to be passed into bafDrift() function |
dataset |
Either 'CCLE', 'GDSC', ro 'GNE' |
snp6.dat |
SNP6 probeset genomic position, accessible from CCLid::ccl_table |
A list containing the fraction of genome drifted, as well the significantly drifted regions CNAo
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