motifbreakR (version 1.2.2)

calculatePvalue: Calculate the significance of the matches for the reference and alternate alleles for the for their PWM

Description

Calculate the significance of the matches for the reference and alternate alleles for the for their PWM

Usage

calculatePvalue(results, background = c(A = 0.25, C = 0.25, G = 0.25, T =
  0.25))

Arguments

results

The output of motifbreakR that was run with filterp=TRUE

background

Numeric Vector; the background probabilites of the nucleotides

Value

• a GRanges object. The same Granges object that was input as results, but with Refpvalue and Altpvalue columns in the output modified from NA to the p-value calculated by TFMsc2pv.

source

H{'e}l{`e}ne Touzet and Jean-St{'e}phane Varr{'e} (2007) Efficient and accurate P-value computation for Position Weight Matrices. Algorithms for Molecular Biology, 2: 15.

Details

This function is intended to be used on a selection of results produced by motifbreakR, and this can be (although not always) a very memory and time intensive process if the algorithm doesn't converge rapidly.

See Also

See TFMsc2pv from the TFMPvalue package for information about how the p-values are calculated.

Examples

data(example.results)
rs2661839 <- example.results[names(example.results) %in% "rs2661839"]
rs2661839 <- calculatePvalue(rs2661839)