filter_total_umi: Get filter for total umis per barcode based on log...

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 total_umi, uses log transformed values for deciding cutoffs.

Usage

filter_total_umi(sce, nmads, type, column = "total_umi")

Arguments

sce	SingleCellExperiment object
nmads	number of median absolute deviations from the median for cutoff
type	either "both", "lower", or "higher", referring to which side to filter on
column	column in colData containing total UMI count

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.