genomicProfiles: Genomic Profile object

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

Genomic Profile object

Description

genomicProfiles is an S4 object serving two purposes: (i) storing internal computed data and (ii) storing paramter options. This object is parsed through the different steps of the pipeline to facilitate that parsing and changing of paramters.

Usage

genomicProfiles(..., parameterOptions = NULL, genomicProfiles = NULL, ChIPScore = NULL)

Arguments

...	Any of the user available slots in genomicProfiles.
parameterOptions	If some parameters were already previously computed or stored in a parameterOptions, parsing this object will use those values instead of the default ones.
genomicProfiles	If some parameters were already previously computed or stored in a genomicProfiles, parsing this object will use those values instead of the default ones.
ChIPScore	If some parameters were already previously computed or stored in a ChIPScore, parsing this object will use those values instead of the default ones.

Details

The genomicProfiles object serves the purpose of storing, and parsing paramters and computed data between the different steps of the pipeline. When creating a genomicProfiles object it is possible to use previously computed values by simply parsing the object to the constructor function.

Value

Returns a genomicsProfiles object with updated slots for all paramters parsed.

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. 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.

See Also

genomicProfiles

parameterOptions

Examples

PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BEAF-32.pfm")
genomicProfiles()
genomicProfiles(PFM=PFM,PFMFormat="JASPAR")

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