PositionWeightMatrix: Accessor Method for the 'PWM' slot in a 'genomicProfiles'...
In ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

Description Usage Arguments Details Value Author(s) References Examples

Accessor Method for the PWM slot in a genomicProfiles object

1	PositionWeightMatrix(object)

object

object is a genomicProfiles

After creating a genomicProfiles object, it is possible to access the Position Weight Matrix stored in this slot. This slot should always contain something. This slot is either supplied by user or directly computed from a Position Frequency Matrix when supplied.

Returns a matrix in the form of a Position Weight Matrix

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)
#Loading PFM files
PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
#Building genomicProfiles object
GPP<-genomicProfiles(PFM=PFM,PFMFormat="raw")
# Accessing Slot
PositionWeightMatrix(GPP)