cleanphe: Remove undesired phenotypes and LOD results from cross and...

In eqtl: Tools for analyzing eQTL experiments: A complementary to Karl Broman's 'qtl' package for genome-wide analysis

Description

Drops the phenotypes or the LOD results within an object of class cross or scanone respectively. The names of the phenotypes and the lodcolumns to be removed are defined by a character string or regular expression.

Usage

cleanphe(x, string = "Buffer")

Arguments

x	An object of class cross or class scanone containing at least two phenotypes. See 'qtl' package manual for read.cross and scanone functions details.
string	The string which describes the names of the phenotypes or the results to remove. It can be defined as a regular expression or just the name of a column. See grep for details.

Details

This function is useful to systematically dropping phenotypes like buffers or controls existing in microarray data or clean out the scanone results in context of expression QTL mapping. The names of the phenotypes and results from objects of cross and scanone class are column names which are defined by a single string or a regular expression specified by the argument string. The grep function searches the data to be removed as follow:

grep(string,names(x)) when x have class scanone.
grep(string,names(x\$pheno)) when x have class cross.

Value

Returns the input cross or scanone object.

Author(s)

Hamid A. Khalili

See Also

grep,scanone,read.cross

Examples

data(seed10);

# Genotype probabilities and genome scan
## Not run: seed10 <- calc.genoprob( cross=seed10, step=2, off.end=0, error.prob=0, 
	 map.function='kosambi', stepwidth='fixed');
## End(Not run)
out.em <- scanone( seed10, pheno.col=1:50, model='normal', method='hk');

# Clean cross object and genome scan
seed10 <- cleanphe(seed10,'Buffer');
seed10 <- cleanphe(seed10,'ctrl');

out.em <- cleanphe(out.em,'Buffer');
out.em <- cleanphe(out.em,'ctrl');

eqtl documentation built on May 2, 2019, 5:42 a.m.