setGeneFactors: Maps snps to genes

In JEFworks/HoneyBADGER: HMM-integrated Bayesian approach for detecting CNV and LOH events using single-cell RNA-seq data

Description

Maps snps to genes

Usage

setGeneFactors(snps, txdb, fill = TRUE, verbose = TRUE)

Arguments

snps	SNP annotations
txdb	TxDb object (ex. TxDb.Hsapiens.UCSC.hg19.knownGene).
fill	SNPs mapping to genes not annotated in txdb will be given unique IDs
verbose	Verbosity

Examples

data(r)
data(cov.sc)
allele.mats <- setAlleleMats(r, cov.sc)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
geneFactor <- setGeneFactors(allele.mats$snps, TxDb.Hsapiens.UCSC.hg19.knownGene)

JEFworks/HoneyBADGER documentation built on July 24, 2021, 3:01 p.m.