utils.read.dart: Imports DarT data to R

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

Imports DarT data to R

Description

Internal function called by gl.read.dart

Usage

utils.read.dart(
  filename,
  nas = "-",
  topskip = NULL,
  lastmetric = "RepAvg",
  service_row = 1,
  plate_row = 3,
  verbose = NULL
)

Arguments

filename	Path to file (csv file only currently) [required].
nas	A character specifying NAs [default '-'].
topskip	A number specifying the number of rows to be skipped. If not provided the number of rows to be skipped are 'guessed' by the number of rows with '*' at the beginning [default NULL].
lastmetric	Specifies the last non genetic column [default 'RepAvg']. Be sure to check if that is true, otherwise the number of individuals will not match. You can also specify the last column by a number.
service_row	The row number in which the information of the DArT service is contained [default 1].
plate_row	The row number in which the information of the plate location is contained [default 3].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default NULL].

Value

A list of length 5. #dart format (one or two rows) #individuals, #snps, #non genetic metrics, #genetic data (still two line format, rows=snps, columns=individuals)

dartR documentation built on June 8, 2023, 6:48 a.m.