readPhen

phen.file

A character, the field separator in phen file.
The default value is <code>","</code>.

sep.phen

(optional) A character, path to ped file.

ped.file

A character, the field separator in ped file.
The default value is <code>","</code>.

sep.ped

Logical, indicating whether the file contains
the names of the variables as its first line.
The default value is TRUE.

header

logical, indicating whether character vectors to be converted to factors.
The default value is FALSE.

stringsAsFactors

logical, indicating whether the IDs of individuals must be unique.
The default value is TRUE.

id.unique

logical, indicating whether the SEX field must be presented.
The default value is TRUE if <code>ped.file</code> is specified,
and it is FALSE otherwise.

sex.optional


The function reads the phenotype and pedigree data in SOLAR format,
i.e. plain-text tables.


SOLAR is the standard software program to perform linkage and
association mappings of the quantitative trait loci (QTLs) in pedigrees of
arbitrary size and complexity. This package allows the user to exploit the
variance component methods implemented in SOLAR. It automates such routine
operations as formatting pedigree and phenotype data. It also parses the model
output and contains summary and plotting functions for exploration of the
results. In addition, solarius enables parallel computing of the linkage and
association analyses, that makes the calculation of genome-wide scans more
efficient. See <http://solar.txbiomedgenetics.org/> for more information about
SOLAR.

readPhen: Read plain-text table files phen and ped

Description

Usage

Arguments

Value