qc_cell: Quality control in single cell data

In jianhaizhang/spatialHeatmap: spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions

Quality control in single cell data

Description

A meta function for quality control in single-cell RNA-seq data.

Usage

qc_cell(sce, qc.metric = list(threshold = 1), qc.filter = list(nmads = 3))

Arguments

sce	Raw single cell count data in form of SingleCellExperiment.
qc.metric	Quality control arguments in a named list passed to perCellQCMetrics, such as qc.metric=list(threshold=1).
qc.filter	Quality control filtering arguments in a named list passed to perCellQCFilters, such as qc.filter=list(nmads=3).

Value

A SingleCellExperiment object.

Author(s)

Jianhai Zhang [e-mail]
Dr. Thomas Girke [e-mail]

References

Amezquita R, Lun A, Becht E, Carey V, Carpp L, Geistlinger L, Marini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pages H, Smith M, Huber W, Morgan M, Gottardo R, Hicks S (2020). “Orchestrating single-cell analysis with Bioconductor.” Nature Methods, 17, 137–145. https://www.nature.com/articles/s41592-019-0654-x. McCarthy DJ, Campbell KR, Lun ATL, Willis QF (2017). “Scater: pre-processing, quality control, normalisation and visualisation of single-cell RNA-seq data in R.” Bioinformatics, 33, 1179-1186. doi: 10.1093/bioinformatics/btw777.

Examples

library(scran); library(scuttle) 
sce <- mockSCE()
qc_cell(sce, qc.metric=list(subsets=list(Mt=rowData(sce)$featureType=='mito'), threshold=1))

jianhaizhang/spatialHeatmap documentation built on Nov. 28, 2024, 4:44 p.m.