Signac (version 1.1.0)

FindTopFeatures: Find most frequently observed features

Description

Find top binary features for a given assay based on total number of cells containing feature. Can specify a minumum cell count, or a lower percentile bound.

Usage

FindTopFeatures(object, ...)
# S3 method for default
FindTopFeatures(object, assay = NULL, min.cutoff = "q5", verbose = TRUE, ...)
# S3 method for Assay
FindTopFeatures(object, assay = NULL, min.cutoff = "q5", verbose = TRUE, ...)
# S3 method for Seurat
FindTopFeatures(object, assay = NULL, min.cutoff = "q5", verbose = TRUE, ...)

Arguments

object

A Seurat object

...

Arguments passed to other methods

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% most common features as the VariableFeatures for the object. Alternatively, this can be an integer specifying the minumum number of cells containing the feature for the feature to be included in the set of VariableFeatures. For example, setting to 10 will include features in >10 cells in the set of VariableFeatures. If NULL, include all features in VariableFeatures.

verbose

Display messages

Value

Returns a Seurat object

Examples

# NOT RUN {
FindTopFeatures(object = atac_small[['peaks']][])
FindTopFeatures(object = atac_small[['peaks']])
FindTopFeatures(atac_small)
# }