siggenes (version 1.46.0)

findDelta: Finding the Threshold Delta

Description

Computes the value of the threshold Delta for a given FDR or number of genes/variables in a SAM or EBAM analysis.

Usage

findDelta(object, fdr = NULL, genes = NULL, prec = 6, initial = NULL, verbose = FALSE)

Arguments

object

either a SAM or an EBAM object.

fdr

numeric value between 0 and 1 for which the threshold Delta and thus the number of genes/variables should be obtained. Only one of fdr and genes can be specified.

genes

integer specifying the number of genes/variables for which the threshold Delta and thus the estimated FDR should be obtained. Only one of fdr and genes can be specified.

prec

integer indicating the precision of the considered Delta values.

initial

a numeric vector of length two containing the minimum and the maximum value of Delta that is initially used in the search for Delta. Both values must be larger than 0. If object is an EBAM object, both values must also be smaller than or equal to 1. If not specified, the minimum is set to 0.1, and the maximum to either the maximum posterior (EBAM) or the maximum absolute distance between the observed and the corresponding expected values of the test statistic (SAM).

verbose

should more information about the search process be shown?

Value

If a value of Delta is found for the exact value of fdr or genes, then a vector of length 3 consisting of Delta and the corresponding number of genes and the estimated FDR. If such a value is not found, then a matrix with two rows and three columns, where the two rows contain the number of genes/variables and the estimated FDR for the two considered values of Delta that provide the closest upper and lower bounds to the desired FDR (if fdr is specified) or number of genes/variables (if genes is specified.)

See Also

sam, ebam