SNPhood-class
(Package: SNPhood) :
A class to represent, investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data
The class SNPhood stores read count-derived information from NGS files for a set of genomic regions of interest as well as associated metadata. It may additionally contain results of various subsequent analyses and statistical tests. See the description below or the Vignette for more details.
● Data Source:
BioConductor
● Keywords: SNPhood, SNPhood-class,
● Alias: SNPhood-class
●
0 images
|
SNPhood
(Package: SNPhood) :
SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data
For more information and an introduction to the package, see the two vignettes.
● Data Source:
BioConductor
● Keywords: SNPhood,, SNPhood-package
● Alias: SNPhood, SNPhood-package
●
0 images
|
analyzeSNPhood
(Package: SNPhood) :
Main function of emph{SNPhood
analyzeSNPhood is the main function of the SNPhood package. All results, parameters and metadata are stored in an object of class SNPhood.
● Data Source:
BioConductor
● Keywords:
● Alias: analyzeSNPhood
●
0 images
|
Specific elements within the annotation slot may also be extracted by using the elements parameter.
● Data Source:
BioConductor
● Keywords:
● Alias: annotation, annotation,SNPhood-method
●
0 images
|
annotationBins
(Package: SNPhood) :
Get the annotation(names) of the bins in a emph{SNPhood
Return the names of the Bins that are defined in the SNPhood object.
● Data Source:
BioConductor
● Keywords:
● Alias: annotationBins
●
0 images
|
annotationBins2
(Package: SNPhood) :
Get the annotation(names) of bins in a emph{SNPhood
annotationBins2 is a helper function that returns annotation of the bins that are defined in the SNPhood object.
● Data Source:
BioConductor
● Keywords:
● Alias: annotationBins2
●
0 images
|
annotationDatasets
(Package: SNPhood) :
Get the annotation(names) of the datasets in a emph{SNPhood
Return the names of the datasets/individuals that are defined in the SNPhood object.
● Data Source:
BioConductor
● Keywords:
● Alias: annotationDatasets
●
0 images
|
annotationReadGroups
(Package: SNPhood) :
Get the annotation(names) of the read groups in a emph{SNPhood
Return the names of the read groups that are defined in the SNPhood object.
● Data Source:
BioConductor
● Keywords:
● Alias: annotationReadGroups
●
0 images
|
annotationRegions
(Package: SNPhood) :
Get the annotation of SNP regions for a emph{SNPhood
Return the annotation of the SNP regions that are defined in the SNPhood object.
● Data Source:
BioConductor
● Keywords:
● Alias: annotationRegions
●
0 images
|
associateGenotypes
(Package: SNPhood) :
Associate genotypes with user regions from a emph{SNPhood
The function associateGenotypes associates genotypes with SNP regions as defined in a SNPhood object. It is possible to assign genotypes only for a subset of datasets as defined in a SNPhood object. To avoid any ambiguities, a 1:1 for genotype and dataset mapping must be given (ses below).
● Data Source:
BioConductor
● Keywords:
● Alias: associateGenotypes
●
0 images
|
providing 
.