Handy function to extract real cell matrix from
It provides the option to filter out broken cells based on proportion
of mitochondrial gene expressions. The input can also be a sparse matrix
only for cell filtering.
Output object from
Numeric value between 0 and 1. Default:
Character vector. User may specify customized mitochondrial gene IDs to perform the filtering. This should correspond to a subset of row names in raw data.
dgCMatrix count matrix of real cells.
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# Please also refer to the example in function CB2FindCell. # Simulate CB2FindCell output object. library(SummarizedExperiment) data(mbrainSub) mbrainReal <- mbrainSub[,Matrix::colSums(mbrainSub)>500] CBOut <- SummarizedExperiment( list(cell_matrix = mbrainReal[,sample(ncol(mbrainReal), 200, replace = TRUE)])) # Get cell matrix, filtering out barcodes with # more than 10% of counts from mitochondrial genes. RealCell <- GetCellMat(CBOut, MTfilter = 0.1) str(RealCell)
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