KASPar_annotate: KASPar_annotate()

In michaelway/KASParClean: Process KASPar data removing conflicts, negatives, duplicates, unknowns

Description

Converts several KASPar annotated CSV files into a single PED file

Usage

KASPar_annotate(csv, RefMajor = "A2", RefMinor = "A1", rsid = "rs123456",
  direction = NA)

Arguments

csv:	string. name - the prefix of the ped and map file
RefMajor:	string. The reference major allele (e.g. A, G, T, C)
RefMinor:	string. The reference minor allele (e.g. A, G, T, C)
rsid:	string. The SNP identification number (is used to name the output)
direction:	string. The direction of the allele codes (e.g. FWD, REV)

Value

A text file with genotype and allele annotations

Note

This software requires a sample file with the first 6 columns of a ped file

and a map file with the names of variants

Author(s)

Michael Way

michaelway/KASParClean documentation built on May 22, 2019, 9:52 p.m.