combineSCE: Combine a list of SingleCellExperiment objects as one...

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Combine a list of SingleCellExperiment objects as one SingleCellExperiment object

Description

Combine a list of SingleCellExperiment objects as one SingleCellExperiment object

Usage

combineSCE(sceList, by.r = NULL, by.c = NULL, combined = TRUE)

Arguments

sceList	A list contains SingleCellExperiment objects. Currently, combineSCE function only support combining SCE objects with assay in dgCMatrix format. It does not support combining SCE with assay in delayedArray format.
by.r	Specifications of the columns used for merging rowData. If set as NULL, the rownames of rowData tables will be used to merging rowData. Default is NULL.
by.c	Specifications of the columns used for merging colData. If set as NULL, the rownames of colData tables will be used to merging colData. Default is NULL.
combined	logical; if TRUE, it will combine the list of SingleCellExperiment objects and return a SingleCellExperiment. If FALSE, it will return a list of SingleCellExperiment whose rowData, colData, assay and reducedDim data slot are compatible within SCE objects in the list. Default is TRUE.

Value

A SingleCellExperiment object which combines all objects in sceList. The colData is merged.

Examples

data(scExample, package = "singleCellTK")
combinedsce <- combineSCE(list(sce,sce), by.r = NULL, by.c = NULL, combined = TRUE)

compbiomed/singleCellTK documentation built on Feb. 10, 2024, 3:32 a.m.