cape (version 2.0.2)

read.pheno: Read in and format data for analysis by cape

Description

This function reads in data for cape analysis and formats it into an object used by other functions in cape. A single comma-separated file containing both phenotype and genotype data is required. Chromosome and marker locations are required for each marker, and markers are assumed to be in order.

Usage

read.pheno(file.format = c("cape", "csv"), filename = NULL, 
pheno.col = NULL, id.col = 1, delim = ",", na.strings = "-")

Arguments

file.format

A character string indicating which of the accepted formats describes the file to be read in. See Details for specifics.

filename

An optional character string with path name specifying the file to be read in. Omission of this argument will prompt a dialog box for selecting a file.

pheno.col

An optional numeric vector specifying which columns the phenotypes of interest are in. If omitted, all phenotypes are read in.

id.col

An integer indicating in which column the individual IDs are stored.

delim

A character string indicating the delimeter in the data file. The default indicates a comma-separated file (",").

na.strings

The symbol used to denote missing data in the file. Misspecifying this character can lead to errors in processing the file in which cape misstakenly thinks some phenotypes have character values in them.

Value

This function is typically used in conjunction with read.geno and make.data.obj when genotype data are too large to include in the data.obj, but can be used for small data as well. read.pheno initializes the data.obj with the phenotype matrix element "pheno" (see below). After read.geno is run, to read in the genotype data separately, make.data.obj is run to transfer information from the geno.obj to the initialized data.obj.

pheno

A matrix containing the phenotype data for the population. Each phenotype is stored in a column, and individuals are stored in rows.

Details

Phenotype data can be contained in one of two file formats: cape, or csv. For a description of the cape format, see read.population. The csv format must contain the following:

• header: A header labeling each column is required
• phenotypes: All phenotypes are required to be numeric. Phenotypes that are not numeric must be coded numerically. For example sex can be coded as [0,1]. Missing values are indicated with the symbol specified by na.strings. The default symbol for na.strings is '-'

See Also

read.population, read.geno, make.data.obj