PositionFrequencyMatrix_-: Setter method for the 'PFM' slot in a 'genomicProfiles'...

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

Setter method for the PFM slot in a genomicProfiles object

Description

Setter method for the PFM slot in a genomicProfiles object

Usage

PositionFrequencyMatrix(object)<- value

Arguments

object	object is a genomicProfiles object
value	value can be of two forms. Either a matrix in the form of a Position Frequency Matrix or a path/to/file character string.

Details

The Position Frequency Matrix is one of the fundamental object that needs to be supplied to a genomicProfiles. If after building a genomicProfiles, only the Position Frequency Matrix needs to be modified then it is possible to manually update the value of this matrix using the function above. There are two options for the type of data that may be supplied to the PFM slot: a matrix in the form of a Position Frequency Matrix (matrix with four rows - one for each base pair (ACTG) and a number of columns equal to the number of sites in the binding site), or it is possible (also recommended) to provide a path to the file containing the Position Frequency Matrix. This Position Frequency Matrix file may come in multiple form such as RAW, Transfac or JASPAR. WARNING: if a genomicProfiles object has already been created and only the PFM is supplied/updated , then the Positon Weight Matrix will automatically updated as well.

Value

Returns a genomicProfiles with an updated PFM slot (as described above this will lead to an updated PositionWeightMatrix).

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"),"BEAF-32.pfm")
#Building genomicProfiles object
# NOT ADVISED!!!! PLEASE PARSE PFM AND PFMFormat together
GPP<-genomicProfiles(PFMFormat = "JASPAR")
#Setting PFM
PositionFrequencyMatrix(GPP) <- PFM

patrickCNMartin/ChIPanalyser documentation built on Dec. 5, 2024, 9:32 a.m.