singleCellExperiment not working

RausellLab / CelliD

Gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.

GNU General Public License v3.0

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singleCellExperiment not working #1

Closed baj12 closed 4 years ago

baj12 commented 4 years ago

RunMCX is only working with Seurat object and not with SingleCellExperiment objects:

aa = as.SingleCellExperiment(seuratPbmc)
aa= RunMCA(aa, nmcs=5)
RunMCTSNE(aa, dims=seq(5), reduction = "MCA")

Error in reducedDim<-(*tmp*, reduction.name, value = cellEmb) : invalid 'value' in 'reducedDim(, type="character") <- value' 'value' should have number of rows equal to 'ncol(x)'

Cortalak commented 4 years ago

Hello, sorry for the late reply and thanks for noticing that error.

I will update you as soon as this issue is fixed.

Cortalak commented 4 years ago

Hi,

The issue is now fixed. Changed the code for MCX function which was grabbing wrong indexes for SingleCellExperiment object. Thank you for pointing out this bug and again sorry for the late response.