| PositionWeightMatrix<- {ChIPanalyser} | R Documentation |
PositionWeightMatrix slot in a
genomicProfileParameters object
Setter Method for the PositionWeightMatrix slot in a
genomicProfileParameters object
PositionWeightMatrix(object) <- value
object |
|
value |
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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 genomicProfileParameters object has already been created.
In that case, we advise to first create a
genomicProfileParameters 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.
Returns a genomicProfileParameters object with an updated
value for the PWM 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, 84–94.
#Building genomicProfileParameters object
GPP <- genomicProfileParameters()
#Setting PWM to PositionWeightMatrix slot
PWM <- matrix(runif(32,-10,20), ncol=8)
rownames(PWM) <- c("A","C","T","G")
PositionWeightMatrix(GPP) <- PWM