tLOHDataImport: Import VCF for tLOHCalc

In USCDTG/tLOH: Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations

Import VCF for tLOHCalc

Description

Import a VCF with per-cluster allele count information at heterozygous SNP positions for the tLOHCalc calculation function.

Arguments

vcf	An input VCF file. Spatial transcriptomics clusters make up the sample columns. AD and DP fields are required. Each SNP should be annotated with dbSNP rsIDs.

Value

Output is a dataframe with required fields for tLOHCalc

Author(s)

Michelle Webb

Examples

    ## Not run: 
    R.utils::gunzip("inst/extdata/Example.vcf.gz","inst/extdata/Example.vcf")
    exampleDF <- tLOHDataImport("inst/extdata/Example.vcf")
## End(Not run)

USCDTG/tLOH documentation built on Oct. 23, 2022, 8:05 p.m.