genomicProfiles: Genomic Profile object

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/2AllS4Class_ProfileParameters.R

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

1

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 <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<e2><80><93>94.

See Also

genomicProfiles

parameterOptions

Examples

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3
PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
genomicProfiles()
genomicProfiles(PFM=PFM,PFMFormat="raw")

ChIPanalyser documentation built on Nov. 8, 2020, 8:23 p.m.