F1Dosages2Matrix: Convert the F1 dosage scores data.frame or file to polymapR...

In fitPoly: Genotype Calling for Bi-Allelic Marker Assays

Convert the F1 dosage scores data.frame or file to polymapR input matrix

Description

Functions writeDosagefile, compareProbes and removeRedundant produce score files. This function reads such a file and converts the result to a data.frame as needed by the polymapR package.

Usage

F1Dosages2Matrix(dosages, outfile=NA, dec=".", sep=",")

Arguments

dosages	name of an F1 dosage scores file as produced by functions writeDosagefile, compareProbes or removeRedundant, or a data frame read from such a file
outfile	(path and) name of an output file, default NA means that no file is written. The file is written by function writeDatfile; normally using the default parameters but if file extension is 'csv', quote is set to TRUE and the specified dec and sep parameters are used
dec	character to use as decimal separator in the output file, default "."; only used if extension of outfile is 'csv' (otherwise ".")
sep	character to use as field separator in the output file, default ","; only used if extension of outfile is 'csv' (otherwise tab character)

Value

A matrix as needed by the polymapR package: one row per marker, one column per sample, containing integer scores (0 .. ploidy) or NAs. Row names are marker names, column names are sample names; the first two columns are the (consensus) scores of Parent1 and Parent2.
If outfile is not NA also an output file is written: if the extension is 'csv' a csv file is written with the specified decimal and field separators (default '.' and ',') and with row and column names quoted, else a tab-separated file.

fitPoly documentation built on April 3, 2025, 8:58 p.m.