BPFrequency: Accessor method for 'BPFrequency' slot in a 'genomicProfiles'...
In ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

Description Usage Arguments Details Value Author(s) References Examples

Extract or Access BPFrequency slot in a genomicProfiles object.

1	BPFrequency(object)

object

object is a genomicProfiles

Default value is c(0.25,0.25,0.25,0.25) When generating a Postion Weight Matrix from a Position Frequency Matrix, the probability of occurrence of each base pair (Base Pair Frequency) is necessary (as originally described by Gary Stormo). It is possible to set custom values for BPFrequency with a vector of length 4 containing the probability of occurrence of each base pair (A,C,G,T) in order. If Base pair frequency is unknown, BPFrequency will compute base pair frequency from a DNA sequence. The nature of this sequence can be a BSgenome or a DNAStringSet. In order to decrease run time, it is advised to use DNAStringSet

Returns BPFrequency slot in genomicProfiles object.

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.

data(ChIPanalyserData)
# path to Position Frequency Matrix
PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
# Building genomicProfiles object
GPP <- genomicProfiles(PFM=PFM,PFMFormat="raw")
#Extracting BPFrequency slot
BPFrequency(GPP)