GenometriCorrConfig-class: Configuration class '"GenometriCorrConfig"': a list of...

In favorov/GenometriCorr: Genometric Correlation package

Description

An object of this class can be initialized by an .ini file; it is inherited form a namedListlthat contains the full structure of .ini file. It restores the structure by call to print. The GenometriCorr - specific call is run.config(conf) that runs GenometriCorrelation with parameters that are stored in the configuration file, as shown in template-config.ini file in the extdata directory of the GenometriCorr package. For a usage example, see GenometriCorrResult-class

Objects from the Class

Objects can be created by calls of the form new("GenometriCorrConfig", src). The call creates the GenometriCorrConfig object from the file src. The file is read as a list (namedList). Each section is a sub-list; each record is an element of its section list. For the string a=b, a is the name and b is the value; if the string does not contain =, it is read as "".

So,

[foo]
bar=2
tap

will be mapped to: config$foo$bar with value of "2" and config$foo$tap with value of "". The values that are used to configure the GenometriCorrelation are described in the section about run.config method.

Slots

.Data:

Object of class "list" the list of values; the main content of the object.

src:

Object of class "character" the name of the file the object was initiated from

names:

Object of class "character" the names to address the mail list are names of the config file sections. It is inherited from "namedList"

Extends

Class "namedList", directly. Class "list", by class "namedList", distance 2. Class "vector", by class "namedList", distance 3.

Methods

show

signature(object = "GenometriCorrConfig"): prints the .ini file text as a record or for use later as a GenometriCorrConfig.

Note

Here is an example of the .ini file content:

[data]
query=UCSCcpgis_hg19.bed
query.format=bed
reference=UCSCrefseqgenes_hg19.bed
reference.format=bed
mapping=q.bed
do.mapping=FALSE

[chromosomes]
chr1
chr2
chr3

[chromosomes.length]
chr1=249250621
chr2=243199373
chr3=198022430
chr4=191154276
chr5=180915260
chr6=171115067
chr7=159138663
chrX=155270560
chr8=146364022
chr9=141213431
chr10=135534747
chr11=135006516
chr12=133851895
chr13=115169878
chr14=107349540
chr15=102531392
chr16=90354753
chr17=81195210
chr18=78077248
chr20=63025520
chrY=59373566
chr19=59128983
chr22=51304566
chr21=48129895
chrM=16571

[options]
add.chr.as.prefix=FALSE
awhole.only=FALSE
suppress.evaluated.length.warning=FALSE
keep.distributions=TRUE
showTkProgressBar=TRUE
showProgressBar=FALSE

[tests]
permut.number=100
#the same as
#ecdf.area.permut.number=100
#mean.distance.permut.number=100
#jaccard.measure.permut.number=100

Author(s)

Alexander Favorov [e-mail], Loris Mularoni, Yulia Medvedeva, Harris A. Jaffee, Ekaterina V. Zhuravleva, Veronica Busa, Leslie M. Cope, Andrey A. Mironov, Vsevolod J. Makeev, Sarah J. Wheelan

References

http://genometricorr.sourceforge.net/

See Also

The GenometriCorrResult-class class; the GenometriCorr documentation and the GenometriCorr package vignette.

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