get_outliers: get_outliers

In wmacnair/SampleQC: Robust, multivariate, multi-sample, multi-celltype QC for single cell RNA-seq data

get_outliers

Description

Extracts list of outliers

Usage

get_outliers(qc_obj, exc_groups = NULL, exc_clusters = NULL)

Arguments

qc_obj	Output from fit_sampleqc
exc_groups	(optional) List of sample groups to exclude.
exc_clusters	(optional) List of clusters to exclude. This is intended for use when there are groups of cells with sufficient numbers to be modelled as a group by SampleQC, but the user wishes to exclude them (for example, a large cluster of cells with extremely high mitochondrial proportions). In this case, fit_sampleqc would identify these as a valid celltype / mixture component and not outliers. Specifying exc_clusters allows these to be removed, e.g. exc_clusters= list(SG2=c(2,3)) would specify removing components 2 and 3 in sample group SG2.

Value

data.table containing cell_id, sample_id and whether outlier or not

wmacnair/SampleQC documentation built on Nov. 18, 2022, 5 p.m.