Remove undesired phenotypes and LOD results from cross and scanone object respectively
Drops the phenotypes or the LOD results within an object of class
scanone respectively. The names of the phenotypes and the lodcolumns to be removed are defined by a character string or regular expression.
cleanphe(x, string = "Buffer")
An object of class
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
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
scanone class are column names which are defined by a single string or a regular expression specified by the argument
grep function searches the data to be removed as follow:
grep(string,names(x)) when x have class
grep(string,names(x\$pheno)) when x have class
Returns the input cross or scanone object.
Hamid A. Khalili
1 2 3 4 5 6 7 8 9 10 11 12 13 14
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');
Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.