mergeSparseAll {rliger}

Merge matrices while keeping the union of rows

Description

mergeSparseAll takes in a list of DGEs, with genes as rows and cells as columns, and merges them into a single DGE. Also adds libraryNames to colnames from each DGE if expected to be overlap (common with 10X barcodes). Values in rawData or normData slot of a ligerDataset object can be processed with this.

For a list of dense matrices, usually the values in scaleData slot of a ligerDataset object, please use mergeDenseAll which works in the same way.

Usage

mergeSparseAll(
  datalist,
  libraryNames = NULL,
  mode = c("union", "intersection")
)

mergeDenseAll(datalist, libraryNames = NULL)

Arguments

datalist

List of dgCMatrix for mergeSparseAll or a list of matrix for mergeDenseAll.

libraryNames

Character vector to be added as the prefix for the barcodes in each matrix in datalist. Length should match with the number of matrices. Default NULL do not modify the barcodes.

mode

Whether to take the "union" or "intersection" of features when merging. Default "union".

Value

dgCMatrix or matrix with all barcodes in datalist as columns and the union of genes in datalist as rows.

Examples

rawDataList <- getMatrix(pbmc, "rawData")
merged <- mergeSparseAll(rawDataList, libraryNames = names(pbmc))