importProgeny: Import Data from Progeny

Description Usage Arguments Author(s)

View source: R/importProgeny.r

Description

readInData() imports data exported from a Progeny database.

Usage

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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.