PWMpseudocount_-: Setter Method for the 'pseudocount' slot in a...

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

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 <[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.

Examples

# Loading data
data(ChIPanalyserData)

#Building data objects
GPP <- parameterOptions( PWMpseudocount=0)
#Setting Value for new PWMpseudocount
PWMpseudocount(GPP) <- 1

patrickCNMartin/ChIPanalyserDev documentation built on Nov. 14, 2019, 4:39 p.m.