read_in_sequenom_data: Read in Sequenom Data

In StevisonLab/genotypeR: SNP Genotype Marker Design and Analysis

Description

read_in_sequenom_data reads in a csv file produced from the Sequenom platform (i.e., sequenom excel output saved as a csv).

This function is a wrapper function around read.csv in order to read genotype data from the Sequenom Platform, and provide data compatible with the genotypeR package.

Usage

read_in_sequenom_data(x, sort_char = "chr|contig", ...)

Arguments

x	This is a csv formatted Genotypes tab of exported sequenom data that you would like to read in.
sort_char	is the character string output by the PERL pipeline in the marker design phase (i.e., chr 1000 1050 AAA[A/T]GTC; the chr is the sort_char. Defaults to chr or contig.
...	Other arguments passed to the function

Value

A data frame suited for the genotypeR package

Examples

sequenom_file <- system.file("extdata/sequenom_test_data.csv", package = "genotypeR")

sequenom_data <- read_in_sequenom_data(sequenom_file)

StevisonLab/genotypeR documentation built on May 5, 2019, 8 p.m.