Example data: Allele counts at variation positions

Data frames of allele counts at variant positions per cell. Variant positions can be either common single nucleotide polymorphisms (SNPs) positions or individual-specific heterozygous positions retrieved by bulk sequencing.

Usage

allele_counts_atac_tumor

allele_counts_atac_ref

allele_counts_rna_tumor

allele_counts_rna_ref

Format

A data frame with columns based on the Variant Call Format (VCF) columns. It contains the following columns:

cell

Barcodes of cells (character).

id

Variant unique identifier defined as CHROM_POS_REF_ALT, e.g. "1_920949_C_G" (character).

CHROM

Chromosome in integer format, e.g. 15 (X and Y chromosomes are not included) (integer).

POS

Position of the variant (1-base positions) (integer).

REF

Reference allele base, "A" "C" "G" or "T" (character).

ALT

Alternative allele base, "A" "C" "G" or "T" (character).

RD

Reference allele depth/count (integer).

AD

Alternative allele depth/count (integer).

DP

Total depth/count (integer).

GT

Genotype: "0/1" or "1/0" if unphased; "0|1" or "1|0" if phased. (character).

See also

• process_allele()