load_cellSNP_vcf: Load sparse matrices A and D from cellSNP VCF file with...

In single-cell-genetics/cardelino: Clone Identification from Single Cell Data

Load sparse matrices A and D from cellSNP VCF file with filtering SNPs

Description

Load sparse matrices A and D from cellSNP VCF file with filtering SNPs

Usage

load_cellSNP_vcf(
  vcf_file,
  min_count = 0,
  min_MAF = 0,
  max_other_allele = NULL,
  rowname_format = "full",
  keep_GL = FALSE
)

Arguments

vcf_file	character(1), path to VCF file generated from cellSNP
min_count	minimum count across all cells, e.g., 20
min_MAF	minimum minor allele fraction, e.g., 0.1
max_other_allele	maximum ratio of other alleles comparing to REF and ALT alleles; for cellSNP vcf, we recommend 0.05
rowname_format	the format of rowname: NULL is the default from vcfR, short is CHROM_POS, and full is CHROM_POS_REF_ALT
keep_GL	logical(1), if TRUE, check if GL (genotype probability) exists it will be returned

Value

A list with elements the matrices A and D and GL, the genotype probability. If keep_GL is false the GL element will be an empty list.

Examples

vcf_file <- system.file("extdata", "cellSNP.cells.vcf.gz",
    package = "cardelino"
)
input_data <- load_cellSNP_vcf(vcf_file)

single-cell-genetics/cardelino documentation built on Nov. 22, 2022, 4:05 p.m.