importProgeny: Import Data from Progeny

In mackerman44/idfgen: Import, Manipulate, and Export Genotype Data

Description

readInData() imports data exported from a Progeny database.

Usage

importProgeny(inputFile, genotypeStartColumn, popColumn = 1,
  sortBPs = FALSE)

Arguments

inputFile	the .txt file containing the biological and genotype data to be imported into idfgen. The data exported from Progeny should be in the following format. Export Format: Wide (One Row per Individual); Identification: Unique ID = Individual Name & Export Using Pedigree and ID; Allele Format: Two Columns Per Call & Export No Calls as "0"; SNP Coding: A,C,G,T; Allele Call: 142,144,146; Pedigree Options: Use pedigree names. Any additional fields may be added.
genotypeStartColumn	the column # in inputFile where the genotypes begin. This will vary depending on the number of additional fields added to the Progeny export.
popColumn	which column in inputFile would you like to use to parse the data. The default is 1, which is where Progeny exports Pedigree names
sortBPs	the readInData() function will check for "AB"-"BA" discrepancies. If sortBPs = TRUE, then any "BA" genotypes will automatically be converted to "AB"

Author(s)

Eric Grau and Mike Ackerman

mackerman44/idfgen documentation built on May 21, 2019, 10:51 a.m.