Flexible and efficient genotype file reading with autodetection using fread

Source: R/getGeno.R

Allows flexible import of SNP genotype data from Illumina FinalReport files, using fast initial column detection via data.table::fread, followed by full genotype matrix construction with snpStats::read.snps.long.

getGeno(...)

# S4 method for class 'ANY'
getGeno(
  path,
  fields = list(sample = 2, snp = 1, allele1 = 7, allele2 = 8, confidence = 9),
  codes = c("A", "B"),
  threshold = 0.15,
  sep = "\t",
  skip = 0,
  verbose = TRUE,
  every = NULL
)

Arguments

...

Additional optional arguments.

path

Path to the directory containing FinalReport.txt

fields

List specifying column indices (sample, snp, allele1, allele2, confidence)

codes

Allele codes (e.g., c("A", "B"))

threshold

Confidence threshold

sep

Field separator

skip

Lines to skip

verbose

Logical; show progress

every

Frequency for progress updates

Value

An SNPDataLong object