PFMFormat: Accesor method for the 'PFMFormat' slot in a...
In ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

Description Usage Arguments Details Value Author(s) References Examples

Accesor method for the PFMFormat slot in a genomicProfiles object

1	PFMFormat(object)

object

object is a genomicProfiles object

If loading a PositionFrequencyMatrix from a file, the format of the file should be specified. Default is raw. Please keep in mind that this argument is used when parsing the PositionFrequencyMatrix file. IF this argument is changed after building the genomicProfiles with a PositionFrequencyMatrix file, this will not influence the parsing of the file. PFMFormat can be one of the following: "raw","transfac","JASPAR" or "sequences"

Returns the value assigned to the PFMFormat slot a genomicProfiles

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 data objects
#### THIS IS THE PREFFERED METHOD FOR SETTING PFMFormat
GPP <- genomicProfiles(PFM=PFM,PFMFormat="raw")
#Setting New value for PFMFormat
PFMFormat(GPP)