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

Description Usage Arguments Details Value Author(s) References Examples

Setter method for the PFMFormat slot in a genomicProfiles object

1	PFMFormat(object) <- value

`object`	`object` is a `genomicProfiles` object
`value`	`value` is character string of one of the following: "raw","transfac","JASPAR" or "sequences". If loading a `PositionFrequencyMatrix` from a file, the format of the file should specified. Default is raw.

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.

Returns a genomicProfiles object with an updated value for the PFMFormat 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.

# 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) <- "raw"