checkGenotypes

checkGenotypes checks genotyping data for common errors in readGenotypes output.

checkGenotypes(
  geno_data,
  fulc_data,
  return_geno = TRUE,
  return_flags = FALSE,
  target_sp = c("Caenorhabditis briggsae", "Caenorhabditis elegans",
    "Caenorhabditis tropicalis"),
  profile = "general"
)

Arguments

geno_data

a genotyping dataframe generated from the readGenotypes function.

fulc_data

a single, joined fulcrum dataframe with all collection data.

return_geno

logical, if TRUE the genotyping data is returned.

return_flags

logical, if TRUE the rows of data for specific flags are returned.

target_sp

vector of target species for species id checks. Default target species names are: Caenorhabditis briggsae, Caenorhabditis elegans, Caenorhabditis tropicalis. target_sp parameter is only required when the profile parameter is set to "nematode".

profile

set to "general" to use a basic genotyping sheet with basic functionality. Set to "nematode" to use the nematode specific genotyping sheet and the standard Andersen Lab functionality.

Value

a list of flagged rows in genotyping and fulcrum dataframes for each flag.