cleanphe {eqtl} | R Documentation |
Drop the phenotypes or the LOD results within an object of class cross
or scanone
respectively. The names of the phenotypes and the lodcolumns to remove are defined by a character string or a regular expression.
cleanphe(x, string = "Buffer")
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. |
This function is useful to systematically drop 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 the results from objects of class cross
and class scanone
are column names which are defined by a single string or a regular expression specified by the argument string
.
The data to remove are searched by the grep
function as follow:
grep(string,names(x))
when x have class scanone
.grep(string,names(x$pheno))
when x have class cross
.Return the input cross or scanone object.
Hamid A. Khalili
data(seed10); # Genotype probabilities and genome scan seed10 <- calc.genoprob( cross=seed10, step=2, off.end=0, error.prob=0, map.function='kosambi', stepwidth='fixed'); out.em <- scanone( seed10, pheno.col=1:50, model='normal', method='em'); # 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');