readInData: read in data from a Progeny-style output file or...

In delomast/EFGLmh: Functions For Working With Microhaps for EFGL

read in data from a Progeny-style output file or matrix/dataframe/tibble adn create an EFGLdata object

Description

read in data from a Progeny-style output file or matrix/dataframe/tibble adn create an EFGLdata object

Usage

readInData(
  input,
  genotypeStart = NULL,
  pedigreeColumn = 1,
  nameColumn = 2,
  convertNames = TRUE,
  convertMetaDataNames = TRUE,
  missingAlleles = c("0", "00", "000"),
  guess_max = 10000
)

Arguments

input	Either a character string to the tab-separated input file with a header row or a matrix/dataframe/tibble. Structure of the input: one row per individual. One column giving pedigree (population) names, one column giving individual names, optional additional metadata columns, genotype columns. Pedigree and individual name columns can be anywhere, if specified. Genotype columns MUST be consecutive and be the right most columns. Genotypes are given as two columns per call (diploidy assumed).
genotypeStart	The column number that genotypes start at. If not specified, the first column with a column name ending in ".A1", ".a1", "-A1", or "-a1" is chosen.
pedigreeColumn	The column number that contains pedigree (population) names.
nameColumn	The column number that contains individual names. These MUST be unique.
convertNames	TRUE to convert genotype and pedigree names in the same way that IDFGEN does (remove special characters from both and remove "." from genotype names).
convertMetaDataNames	TRUE to remove special characters and spaces from metadata column names. This makes accessing them easier.
missingAlleles	a vector of values (not NA) to treat as missing alleles. They will be converted to NA.
guess_max	If input is a character string, this is the maximum number of lines to use when guessing input data types. Making this smaller results in quicker loading, making it larger can fix some parsing errors

Value

An EFGLdata object, which is just a list with two elements. The first element is a tibble with genotype data, the second is a tibble with metadata

delomast/EFGLmh documentation built on June 1, 2024, 6:55 a.m.