getRegionsScores: Get region scores
In aertslab/cisTopic: cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
View source: R/BasicTopicOperations.R
getRegionsScores R Documentation
Get region scores
Description
Get region scores per topic
Usage
getRegionsScores(object, method = "Z-score", scaled = TRUE)
Arguments
object
Initialized cisTopic object, after the object@selected.model has been filled.
method
Select the method for processing the region assignments: 'Z-score','Probability' or 'NormTop'.
rescale
Whether feature scaling should be performed within the topics. By default, it is set to true.
Details
'Z-score' computes the Z-score for each topic assingment per cell/region. 'Probability' divides the topic assignments by the total number
of assignments in the cell/region in the last iteration plus alpha. If using 'NormTop', regions are given an score defined by: \beta_{w, k} (\log
\beta_{w,k} - 1 / K \sum_{k'} \log \beta_{w,k'}).
Value
Returns the region scores per topic in object@region.data.
aertslab/cisTopic documentation built on April 6, 2024, 9:31 p.m.
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View source: R/BasicTopicOperations.R
| getRegionsScores | R Documentation |
Get region scores
Description
Get region scores per topic
Usage
getRegionsScores(object, method = "Z-score", scaled = TRUE)
Arguments
object |
Initialized cisTopic object, after the object@selected.model has been filled. |
method |
Select the method for processing the region assignments: 'Z-score','Probability' or 'NormTop'. |
rescale |
Whether feature scaling should be performed within the topics. By default, it is set to true. |
Details
'Z-score' computes the Z-score for each topic assingment per cell/region. 'Probability' divides the topic assignments by the total number
of assignments in the cell/region in the last iteration plus alpha. If using 'NormTop', regions are given an score defined by: \beta_{w, k} (\log
\beta_{w,k} - 1 / K \sum_{k'} \log \beta_{w,k'}).
Value
Returns the region scores per topic in object@region.data.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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