runDM: Calculate Diffusion Components on the cell-cisTopic...

In aertslab/cisTopic: cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data

Calculate Diffusion Components on the cell-cisTopic distributions

Description

Calculate Diffusion Components on the cell-cisTopic distributions

Usage

runDM(object, target, method = "Z-score", seed = 123, ...)

Arguments

object	Initialized cisTopic object, after the [e-mail] has been filled.
target	Whether dimensionality reduction should be applied on cells ('cell') or regions (region). Note that for speed and clarity reasons, dimesionality reduction on regions will only be done using the regions assigned to topics with high confidence (see binarizecisTopics()).
method	Select the method for processing the cell assignments: 'Z-score' and 'Probability'. In the case of regions, an additional method, 'NormTop' is available (see getRegionScores()).
seed	Integer for making the results reproducible.
...	See DiffusionMap from the package destiny.

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 a cisTopic object with the tSNE coordinates stored in object@dr$DM.

aertslab/cisTopic documentation built on April 6, 2024, 9:31 p.m.