Find highly variable ATAC-seq features for a MatisseObject
Source:R/dispatch.R
FindTopFeatures.MatisseObject.RdRuns FindTopFeatures on the embedded Seurat object
and returns the updated MatisseObject. Selects the most accessible
peaks for downstream LSI / UMAP.
Usage
# S3 method for class 'MatisseObject'
FindTopFeatures(object, assay = NULL, min.cutoff = "q5", verbose = TRUE, ...)Arguments
- object
A
MatisseObject.- assay
Name of assay to use
- min.cutoff
Cutoff for feature to be included in the VariableFeatures for the object. This can be a percentile specified as 'q' followed by the minimum percentile, for example 'q5' to set the top 95\ as the VariableFeatures for the object. Alternatively, this can be an integer specifying the minimum number of counts for the feature to be included in the set of VariableFeatures. For example, setting to 10 will include features with >10 total counts in the set of VariableFeatures. If NULL, include all features in VariableFeatures. If NA, VariableFeatures will not be altered, and only the feature metadata will be updated with the total counts and percentile rank for each feature.
- verbose
Display messages
- ...
Additional arguments forwarded to
FindTopFeatures(e.g.min.cutoff).