PWMpseudocount {ChIPanalyser}R Documentation

Accessor Method for a PWMpseudocount slot in a genomicProfileParameters

Description

Accessor Method for a PWMpseudocount slot in a genomicProfileParameters

Usage

PWMpseudocount(object)

Arguments

object

object is a genomicProfileParameters object.

Details

In the context of Position Weight Matricies, the pseudocount is used to avoid 0 probabilities during the transformation of Position Frequency Matrix to a Position Probability Matrix and finally to a Postion Weight Matrix. It is essentially a sample correction that is added in the case of small sample size. The effect of the base pair to which a pseudocount was assigned will not influence the model nor will create mathematical issues such as infinities or zero division. Default is set at 1.

Value

Returns the value assigned to a PWMpseudocount slot in a genomicProfileParameters object

Author(s)

Patrick C. N. Martin <pm16057@essex.ac.uk>

References

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.

Examples

# Loading data
data(ChIPanalyserData)
#Loading PFM files
PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
#Building data objects
GPP <- genomicProfileParameters(PFM=PFM, PWMpseudocount=0)
#Accessing slot value
PWMpseudocount(GPP)

[Package ChIPanalyser version 1.4.0 Index]