sce_cbind {scMerge} | R Documentation |
SingleCellExperiment
objects from different batches/experimentsCombind several SingleCellExperiment
objects from
different batches/experiments.
sce_cbind(sce_list, method = NULL, cut_off_batch = 0.01, cut_off_overall = 0.01, exprs = c("counts", "logcounts"), colData_names = NULL, batch_names = NULL)
sce_list |
A list contains the |
method |
A string indicates the method of combining the gene expression matrix,
either |
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 |
batch_names |
A string vector indicating the batch names for the output sce object |
A SingleCellExperiment
object with the list of SCE objects combined.
Yingxin Lin
library(SingleCellExperiment) 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)