summarise.genomescan: summarise.genomescan

In drmjc/genomics: Genomics related functions.

Description

Function to threshold a pvalue table at various levels, and report how many genes pass those linkage thresholds. You can look at various subsets of genes from within the pval table, by supplying a list argument to 'genes' where each element of the list is a vector of row indices.

Usage

  summarise.genomescan(pvals,
    thresholds = c(0.05, 0.001, 1e-04, 1e-05, 1e-06, 1e-07),
    genes = NULL, file = NULL, which.genes = F,
    which.markers = F)

Arguments

pvals	a GxM matrix, where G is no. of genes, M is no of markers
thresholds	the various levels at which to threshold the data
genes	if NULL, then all genes are used; alternatively, it can be a list of numeric vectors which will be used to index the rows in the pvals table
file	the name of a text file for the results to be written to

Value

if genes == NULL then a named vector of counts of genes that pass the thresholds is produced. If genes != NULL, then a table of counts is produced, with each set of genes in a different appropriately named column.

Author(s)

Mark Cowley, 22 Feb 2006

Examples

## Not run: 
	# summarise.genomescan(brain.M.spt$p, genes=genes, file="brain.M.spt.summary.txt")

## End(Not run)

drmjc/genomics documentation built on May 15, 2019, 2:22 p.m.