gl.read.csv: Reads SNP data from a csv file into a genlight object

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Reads SNP data from a csv file into a genlight object

Description

This script takes SNP genotypes from a csv file, combines them with individual and locus metrics and creates a genlight object.

Usage

gl.read.csv(
  filename,
  transpose = FALSE,
  ind.metafile = NULL,
  loc.metafile = NULL,
  verbose = NULL
)

Arguments

filename	Name of the csv file containing the SNP genotypes [required].
transpose	If TRUE, rows are loci and columns are individuals [default FALSE].
ind.metafile	Name of the csv file containing the metrics for individuals [optional].
loc.metafile	Name of the csv file containing the metrics for loci [optional].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity].

Details

The SNP data need to be in one of two forms. SNPs can be coded 0 for homozygous reference, 2 for homozygous alternate, 1 for heterozygous, and NA for missing values; or the SNP data can be coded A/A, A/C, C/T, G/A etc, and -/- for missing data. In this format, the reference allele is the most frequent allele, as used by DArT. Other formats will throw an error.

The SNP data need to be individuals as rows, labeled, and loci as columns, also labeled. If the orientation is individuals as columns and loci by rows, then set transpose=TRUE.

The individual metrics need to be in a csv file, with headings, with a mandatory id column corresponding exactly to the individual identity labels provided with the SNP data and in the same order.

The locus metadata needs to be in a csv file with headings, with a mandatory column headed AlleleID corresponding exactly to the locus identity labels provided with the SNP data and in the same order.

Note that the locus metadata will be complemented by calculable statistics corresponding to those that would be provided by Diversity Arrays Technology (e.g. CallRate).

Value

A genlight object with the SNP data and associated metadata included.

Author(s)

Custodian: Luis Mijangos – Post to https://groups.google.com/d/forum/dartr

Examples

csv_file <- system.file('extdata','platy_test.csv', package='dartR')
ind_metadata <- system.file('extdata','platy_ind.csv', package='dartR')
gl  <- gl.read.csv(filename = csv_file, ind.metafile = ind_metadata)

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.