pcadapt (version 2.2)

read4pcadapt: pcadapt read function

Description

read4pcadapt is a function which output may be read by the main function pcadapt. It currently supports two formats. The first one is a text file containing the genotype matrix with individuals in rows and genotype markers in columns (same format as for the R package LEA). The second supported format is the .ped format.

Usage

read4pcadapt(x = NULL, option = "genotype", header = FALSE, sep = "",
  transpose = FALSE, mapheader = FALSE, mapsep = "\t",
  na.strings = c("-9", "NA", "NaN"))

Arguments

x

can be a file path or a file name, depending on the chosen option.

option

a character string that specifies the type of data to be read: "genotype" (default), "ped" or "pool".

header

a logical value indicating whether the file contains the names of the variables as its first line.

sep

the field separator character.

transpose

a logical value indicating whether the pooled data has the right format, which is n rows and p columns where n is the number of populations and p is the number of genetic markers.

mapheader

a logical value indicating whether the map file contains the names of the variables as its first line.

mapsep

a character string that specifies the type of separator used when reading the data.

na.strings

a character vector of strings which are to be interpreted as NA values. Blank fields are also considered to be missing values in logical, integer, numeric and complex fields.

Examples

## see also ?pcadapt for examples