PositionWeightMatrix_-: Setter Method for the 'PositionWeightMatrix' slot in a...

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

Setter Method for the PositionWeightMatrix slot in a genomicProfiles object

Description

Setter Method for the PositionWeightMatrix slot in a genomicProfiles object

Usage

PositionWeightMatrix(object) <- value

Arguments

object	object is a genomicProfiles object
value	value is a matrix in the form of a Position Weight Matrix.

Details

If a Position Weight Matrix is readily available, it is possible to directly assign this matrix to the PWM slot. However, this is only possible if a genomicProfiles object has already been created. In that case, we advise to first create a genomicProfiles object. It should be noted that this Position Weight Matrix will be automatically computed from a Position Frequency Matrix. If no Position Frequency Matrix are available, then a Position Weight Matrix can be directly assigned to this slot.

Value

Returns a genomicProfiles object with an updated value for the PWM 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. 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

#Building genomicProfiles object
GPP <- genomicProfiles()
#Setting PWM to PositionWeightMatrix slot
PWM <- matrix(runif(32,-10,20), ncol=8)
rownames(PWM) <- c("A","C","T","G")
PositionWeightMatrix(GPP) <- PWM

patrickCNMartin/ChIPanalyser documentation built on Nov. 24, 2022, 12:02 a.m.