Process allele counts results from SCReadCounts format

This function reformats SCReadCounts output into a standardized VCF-like data frame and optionally merges unphased/phased genotype information from a VCF-format data frame.

Usage

process_allele(data, vcf = NULL, samplename = NULL)

Arguments

data

A data frame of SCReadCounts output table (data.frame).

vcf

An optional VCF-format data frame with unphased/phased genotype information to add it in output (data.frame).

samplename

An optional sample name to prefix cell barcodes (character).

Value

A cleaned data frame with VCF-like standardized 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 (if vcf provided): "0/1" or "1/0" if unphased; "0|1" or "1|0" if phased. (character).

Note

• SCReadCounts website

• Variant Call Format (VCF) format

References

SCReadCounts

Liu, H., Bousounis, P., Movassagh, M., Edwards, N., and Horvath, A. SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data. BMC Genomics 22, 689 (2021). doi: 10.1186/s12864-021-07974-8

Examples

# Example data
sc_data <- data.frame(
  ReadGroup = c("cell1", "cell2"),
  CHROM = c(1, 1),
  POS = c(1001, 1002),
  REF = c("A", "C"),
  ALT = c("G", "T"),
  SNVCount = c(3, 5),
  RefCount = c(7, 5),
  GoodReads = c(10, 10)
)

vcf_data <- data.frame(
  CHROM = c(1, 1),
  POS = c(1001, 1002),
  ID = c(".", "."),
  REF = c("A", "C"),
  ALT = c("G", "T"),
  QUAL = c(".", "."),
  FILTER = c(".", "."),
  INFO = c(".", "."),
  FORMAT = c("GT", "GT"),
  sample1 = c("0|1", "1|0"),
  stringsAsFactors = FALSE
)

data <- process_allele(sc_data, vcf = vcf_data, samplename = "sampleA")