sce_cbind: Combind several 'SingleCellExperiment' objects from different...
In SydneyBioX/scMerge: scMerge: Merging multiple batches of scRNA-seq data

sce_cbind

R Documentation

Combind several `SingleCellExperiment` objects from different batches/experiments

Description

Combind several SingleCellExperiment objects from different batches/experiments.

Usage

sce_cbind(
  sce_list,
  method = "intersect",
  cut_off_batch = 0.01,
  cut_off_overall = 0.01,
  exprs = c("counts", "logcounts"),
  colData_names = NULL,
  batch_names = NULL
)

Arguments

`sce_list`	A list contains the `SingleCellExperiment` Object from each batch
`method`	A string indicates the method of combining the gene expression matrix, either `union` or `intersect`. Default to `intersect`. `union` only supports matrix class.
`cut_off_batch`	A numeric vector indicating the cut-off for the proportion of a gene is expressed within each batch
`cut_off_overall`	A numeric vector indicating the cut-off for the proportion of a gene is expressed overall data
`exprs`	A string vector indicating the expression matrices to be combined. The first assay named will be used to determine the proportion of zeores.
`colData_names`	A string vector indicating the `colData` that are combined
`batch_names`	A string vector indicating the batch names for the output sce object

Value

A SingleCellExperiment object with the list of SCE objects combined.

Author(s)

Yingxin Lin

Examples

data('example_sce', package = 'scMerge')
batch_names<-unique(example_sce$batch)
sce_list<-list(example_sce[,example_sce$batch=='batch2'],
               example_sce[,example_sce$batch=='batch3'])
sce_combine<-sce_cbind(sce_list,batch_names=batch_names)

SydneyBioX/scMerge documentation built on April 14, 2024, 3:22 a.m.