FindTopFeatures: Find most frequently observed features

In timoast/signac: Analysis of Single-Cell Chromatin Data

Find most frequently observed features

Description

Find top features for a given assay based on total number of counts for the feature. Can specify a minimum cell count, or a lower percentile bound to determine the set of variable features. Running this function will store the total counts and percentile rank for each feature in the feature metadata for the assay. To only compute the feature metadata, without changing the variable features for the assay, set min.cutoff=NA.

Usage

FindTopFeatures(object, ...)

## Default S3 method:
FindTopFeatures(object, assay = NULL, min.cutoff = "q5", verbose = TRUE, ...)

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

## S3 method for class 'StdAssay'
FindTopFeatures(object, assay = NULL, min.cutoff = "q5", verbose = TRUE, ...)

## S3 method for class '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 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

Value

Returns a Seurat object

Examples

FindTopFeatures(object = atac_small[['peaks']]['data'])
FindTopFeatures(object = atac_small[['peaks']])
FindTopFeatures(object = atac_small[['peaks']])
FindTopFeatures(atac_small)

timoast/signac documentation built on Aug. 23, 2024, 1:48 a.m.