genomicProfiles {ChIPanalyser} | R Documentation

## 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 <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.

### See Also

`genomicProfiles`

`parameterOptions`

### Examples

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

[Package ChIPanalyser version 1.14.0 Index]