PositionFrequencyMatrix {ChIPanalyser} | R Documentation |
PFM
slot in a
genomicProfiles
object
Accessor method for the PFM
slot in a
genomicProfiles
object
PositionFrequencyMatrix(object)
object |
|
After creating a genomicProfiles
object,
it is possible to access the Position Frequency Matrix slot.
However this slot will be empty if the genomicProfiles
object was built using directly a Position Weight Matrix.
See genomicProfiles
Returns the Position Frequency Matrix (PFM
slot) used to compute the
PositionWeightMatrix
in a
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, 84–94.
#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 PositionFrequencyMatrix(GPP)