run.config-methods: Method for Function 'run.config' in Package 'GenometriCorr'
In favorov/GenometriCorr: Genometric Correlation package

The run.config function runs on a "GenometriCorrConfig" class object; it runs the GenometriCorrelation function with the parameters described in the configuration object. The resulting object of "GenometriCorrResult" has the original options in its config slot.

signature(conf = "GenometriCorrConfig"): run.config(conf,query=NA,reference=NA,query.format=NA,reference.format=NA,mapping=NA,mapping.format=NA,do.mapping=NA)
runs GenometriCorrelation.
conf is the "GenometriCorrConfig" class. Its slots correspond to the configuration file sections. Below is the list of the sections and the variables of the file and the corresponding parameters of the GenometriCorrelation

call.

Section	Value	Role
`[chromosomes]`		this section contains the list of chromosomes, it is passed as `chromosomes.to.proceed`
`[chromosomes.length]`	`name=length`	this length will be passed in the `chromosomes.length` parameter in the `['name']` element
`[options]`	`add.chr.as.prefix`	`add.chr.as.prefix`
`[options]`	`awhole.only`	`awhole.only`
`[options]`	`suppress.evaluated.length.warning`	`suppress.evaluated.length.warning`
`[options]`	`keep.distributions`	`keep.distributions`
`[options]`	`showTkProgressBar`	`showTkProgressBar`
`[options]`	`showProgressBar`	`showProgressBar`
`[tests]`	`permut.number`	`permut.number`
`[tests]`	`ecdf.area.permut.number`	`ecdf.area.permut.number`
`[tests]`	`mean.distance.permut.number`	`mean.distance.permut.number`
`[tests]`	`jaccard.measure.permut.number`	`jaccard.measure.permut.number`
`[tests]`	`random.seed`	value to seed the random generator (for reproducibility)

Below are values that describe the input data; they can be overriden by the run.config call parameters.

Section	Value	Role
`[data]`	`query`	name of the query file
`[data]`	`query.format`	format of the file or `'R.variable.name'`
`[data]`	`reference`	name of the reference file
`[data]`	`reference.format`	format of the file or `'R.variable.name'`
`[data]`	`mapping`	name of the mapping file
`[data]`	`mapping.format`	format of the mapping file or `'R.variable.name'`
`[data]`	`do.mapping`	logical; whether to do mapping

Each of the data (query, reference, mapping) parameters may instead be data of one of the accepted formats (GRanges). In this case, the corresponding format value is omitted and nothing is written to the config slot of the result, and the data are used for the function calls. If the format parameter is 'R.variable.name', the input is taken from that variable. The calculation is the same as for GRanges parameter, but the name of the variable and the 'R.variable.name' are saved in config slot of the result.

Other formats are interpreted as format parameters for the import function from rtracklayer package.

See an example at GenometriCorrResult help.

Alexander Favorov favorov@sensi.org, Loris Mularoni, Yulia Medvedeva, Harris A. Jaffee, Ekaterina V. Zhuravleva, Veronica Busa,Leslie M. Cope, Andrey A. Mironov, Vsevolod J. Makeev, Sarah J. Wheelan

favorov/GenometriCorr documentation built on March 30, 2021, 5:21 p.m.