Example data: Allele counts at variant 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 using bulk sequencing. Only chromosomes 3, 4 and 8 are present in the exdata example dataset.

Usage

exdata_allele_counts_atac_tumor

exdata_allele_counts_atac_ref

exdata_allele_counts_rna_tumor

exdata_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.
id: Variant unique identifier defined as CHROM_POS_REF_ALT, e.g. "3_3126620_T_G".
CHROM: Chromosome names, e.g. "3", "X".
POS: Position of the variant (1-base positions).
REF: Reference allele base, "A" "C" "G" or "T".
ALT: Alternative allele base, "A" "C" "G" or "T".
RD: Reference allele depth/count.
AD: Alternative allele depth/count.
DP: Total depth/count.
GT: Genotype: "0/1" or "1/0" if unphased; "0|1" or "1|0" if phased.

Usage

Format

See also