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

Description Usage Arguments Details Value Author(s) References Examples

Setter Method for the pseudocount slot in a parameterOptions object

1	PWMpseudocount(object) <- value

`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

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.

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

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

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84<e2><80><93>94.

# Loading data
data(ChIPanalyserData)

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