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Read and Standardize Allelic Imbalance Data

Source: R/AIsegmentation.R
ReadAI.Rd

Reads allelic imbalance (AI) data from different input formats and standardizes the output.

Usage

ReadAI(aitype, ballele, minsnpcov, gender)

Arguments

aitype

Character. Type of AI input file. Supported values are:

  • "gatk": Tab-separated file with columns Chromosome, Pos, REF_NUCLEOTIDE, ALT_NUCLEOTIDE, REF_COUNT, ALT_COUNT.

  • "dragen": the input must include columns contig, start, stop, refAllele, allele1, allele2, allele1Count, allele2Count, allele1AF, and allele2AF.

  • "other": Tab-separated file with columns Chromosome, Pos, REF_NUCLEOTIDE, ALT_NUCLEOTIDE, REF_COUNT, ALT_COUNT.

ballele

Character. Path to the input allelic count file.

minsnpcov

Numeric, minimum coverage of SNPs to included (default: 20).

gender

Character. Sample gender, either "female" or "male". This value is passed to ReadAI().

Value

A data frame with columns Chromosome, Pos, ref_count, alt_count and maf, containing only autosomal positions (Chromosome not X or Y), with minor allele frequency (maf) between 0 and 0.5.

Examples

if (FALSE) { # \dontrun{
# Read AI data from a count file
maf_df <- ReadAI("gatk", "sample.allele_counts", 20, "female")

# Read AI data from a DRAGEN file
maf_df <- ReadAI("dragen", "sample_dragen.tumor.ballele.counts.gz",20, "female")

# Read AI data from a BAF file
maf_df <- ReadAI("other", "sample.tsv",20, "female")
} # }