R: Utility to import DarT data to R

utils.read.dart {dartR.base}

R Documentation

Utility to import DarT data to R

Description

WARNING: UTILITY SCRIPTS ARE FOR INTERNAL USE ONLY AND SHOULD NOT BE USED BY END USERS AS THEIR USE OUT OF CONTEXT COULD LEAD TO UNPREDICTABLE OUTCOMES.

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].

Details

Internal function called by gl.read.dart()

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)

Author(s)

Custodian: Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)