filter_pct_mito: Get filter for percentage of mitochondrial reads expressed...

In keshav-motwani/scanalysis: Multi-Sample Visualization and Immune Repertoire Analysis Utilities for Single-Cell Data

Description

Wrapper around scater::isOutlier, arguments type and nmads refer to the same thing. For mitochondrial reads, uses non-log transformed values for deciding cutoffs.

Usage

filter_pct_mito(sce, nmads, type, column = "pct_mito")

Arguments

sce	SingleCellExperiment object
nmads	number of median absolute deviations from the median
type	either "both", "lower", or "higher", referring to which side to filter on
column	column in colData containing percentage of mitochondrial reads

Details

Ensure that add_pct_gene has been run before this or that a column named pct_mito is present in colData(sce)

Value

Boolean filter with TRUE for cells and FALSE for outliers. Contains attribute with number of median absolute deviations specified.

Examples

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keshav-motwani/scanalysis documentation built on Feb. 4, 2021, 2:21 a.m.