preprocess_allele: Preprocess allele data

In numbat: Haplotype-Aware CNV Analysis from scRNA-Seq

Preprocess allele data

Description

Preprocess allele data

Usage

preprocess_allele(sample, vcf_pu, vcf_phased, AD, DP, barcodes, gtf, gmap)

Arguments

sample	character Sample label
vcf_pu	dataframe Pileup VCF from cell-snp-lite
vcf_phased	dataframe Phased VCF from eagle2
AD	dgTMatrix Alt allele depth matrix from pileup
DP	dgTMatrix Total allele depth matrix from pileup
barcodes	vector List of barcodes from pileup
gtf	dataframe Transcript GTF
gmap	dataframe Genetic map

Value

dataframe Allele counts by cell

numbat documentation built on May 29, 2024, 1:29 a.m.