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

PFMFormat<-

R Documentation

Setter method for the `PFMFormat` slot in a `genomicProfiles` object

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 JASPAR.

Details

If loading a PositionFrequencyMatrix from a file, the format of the file should be specified. Default is JASPAR. 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 <pm16057@essex.ac.uk>

References

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94. Patrick C.N. Martin and Nicolae Radu Zabe (2020) Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. CSBJ, 18, 3590-3605.

Examples

# Loading data
data(ChIPanalyserData)
#Loading PFM files
PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BEAF-32.pfm")
#Building data objects
#### THIS IS THE PREFFERED METHOD FOR SETTING PFMFormat
GPP <- genomicProfiles(PFM=PFM,PFMFormat="JASPAR")
#Setting New value for PFMFormat
PFMFormat(GPP) <- "JASPAR"

patrickCNMartin/ChIPanalyser documentation built on Nov. 24, 2022, 12:02 a.m.