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Process files created by EFM

process_efm_files.Rd

Subsets the EFM files by contributor (C1/C2)

Usage

process_efm_files(
  x,
  contrib,
  ref,
  minimum_snps,
  A1min,
  A1max,
  A2min,
  A2max,
  metrics = TRUE,
  filter_missing = FALSE
)

Arguments

x

EFM file

contrib

C1/C2

ref

Reference genotype file

minimum_snps

Minimum number of SNPs required

A1min

Minimum value for allele 1 probability thresholds for calculating metrics

A1max

Maximum value for allele 1 probability thresholds for calculating metrics

A2min

Minimum value for allele 2 probability thresholds for calculating metrics

A2max

Maximum value for allele 2 probability thresholds for calculating metrics

metrics

TRUE/FALSE to calculate validation metrics

filter_missing

TRUE/FALSE to filter SNPs with missing allele 2 values

Value

Data frame containing either calculated metrics (if specified) or data frame containing genotype calls