PWMpseudocount: Accessor Method for a 'PWMpseudocount' slot in a...

In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

Accessor Method for a PWMpseudocount slot in a parameterOptions

Description

Accessor Method for a PWMpseudocount slot in a parameterOptions

Usage

PWMpseudocount(object)

Arguments

object

object is a parameterOptions 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 parameterOptions object

Author(s)

Patrick C. N. Martin <[e-mail]>

References

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94. Patrick C.N. Martin and Nicolae Radu Zabe (2020) Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. CSBJ, 18, 3590-3605.

Examples

# Loading data
data(ChIPanalyserData)

#Building data objects
GPP <- parameterOptions(PWMpseudocount=0)
#Accessing slot value
PWMpseudocount(GPP)

patrickCNMartin/ChIPanalyser documentation built on Dec. 5, 2024, 9:32 a.m.