load_cellSNP_vcf | R Documentation |
Load sparse matrices A and D from cellSNP VCF file with filtering SNPs
load_cellSNP_vcf( vcf_file, min_count = 0, min_MAF = 0, max_other_allele = NULL, rowname_format = "full", keep_GL = FALSE )
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 |
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.
vcf_file <- system.file("extdata", "cellSNP.cells.vcf.gz", package = "cardelino" ) input_data <- load_cellSNP_vcf(vcf_file)
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