PFMFormat_: Setter method for the 'PFMFormat' slot in a 'genomicProfiles'...

In patrickCNMartin/ChIPanalyserDev: ChIPanalyser: Predicting Transcription Factor Binding Sites

Description

Setter method for the PFMFormat slot in a genomicProfiles object

Usage

PFMFormat(object) <- value

Arguments

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.

Details

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.

Value

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

Author(s)

Patrick C. N. Martin <[e-mail]>

References

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.

Examples

# 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"

patrickCNMartin/ChIPanalyserDev documentation built on Nov. 14, 2019, 4:39 p.m.