PWMpseudocount_-: Setter Method for the 'pseudocount' slot in a...
In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

PWMpseudocount<-

R Documentation

Setter Method for the `pseudocount` slot in a `parameterOptions` object

Description

Setter Method for the pseudocount slot in a parameterOptions object

Usage

PWMpseudocount(object) <- value

Arguments

`object`	`object` is a `parameterOptions` object
`value`	`value` is a numeric value that will be assigned to the `pseudocount` slot. Defualt is set at 1

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.

Value

Returns a parameterOptions object with an updated value for the pseudocount slot.

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. 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)
#Setting Value for new PWMpseudocount
PWMpseudocount(GPP) <- 1

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