sce_cbind: Combine SingleCellExperiment Object.

Description Usage Arguments Value Author(s) Examples

View source: R/preprocessing.R

Description

Combind the SingleCellExperiment objects from different batches/experiments

Usage

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sce_cbind(sce_list, method = "union", 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

cut_off_batch

A numeric indicates cut-off for the proportion of a gene is expressed within each batch

cut_off_overall

A numeric indicates the cut-off for the proportion of a gene is expressed overall

exprs

A string vector indicates the exprssion matrix that are combined

colData_names

A string vector indicates the colData that are combined

batch_names

A string vector indicates the batch names

Value

A combined SingleCellExperiment objects

Author(s)

Yingxin Lin

Examples

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require(SingleCellExperiment)
data("sce_mESC", package = "scMerge.data")
batchNames<-unique(sce_mESC$batch)
sce_list<-list(sce_mESC[,sce_mESC$batch==batchNames[1]],
               sce_mESC[,sce_mESC$batch==batchNames[2]],
               sce_mESC[,sce_mESC$batch==batchNames[3]],
               sce_mESC[,sce_mESC$batch==batchNames[4]],
               sce_mESC[,sce_mESC$batch==batchNames[5]])
sce_combine<-sce_cbind(sce_list,batch_names=batchNames)

SydneyBioX/scMerge documentation built on Oct. 9, 2018, 3:28 p.m.