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

Description Usage Arguments Details Value Author(s) References Examples

Setter Method for the PositionWeightMatrix slot in a genomicProfiles object

1	PositionWeightMatrix(object) <- value

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

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.

Returns a genomicProfiles 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<e2><80><93>94.

#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