Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/2AllS4Class_ProfileParameters.R
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.
1 | genomicProfiles(..., parameterOptions = NULL, genomicProfiles = NULL, ChIPScore = NULL)
|
... |
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. |
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.
Returns a genomicsProfiles
object with updated slots for all paramters parsed.
Patrick C. N. Martin <pm16057@essex.ac.uk>
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.
1 2 3 | PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
genomicProfiles()
genomicProfiles(PFM=PFM,PFMFormat="raw")
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