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Description
Dear SINCERA team
I'm trying to use gene-cell matrix with ENSEMBL gene ID and celltype.enrichment function calls error like:
`> sc <- celltype.enrichment(sc, id.type="ENSEMBL", species="HOMSA")
Sincera: cell type enrichment analysis ...
Using differentially expressed genes for cell type enrichment analysis
Number of diff genes ( pvalue < 0.01 ) per cluster
1 2 3 4 5 6 7 8
7133 2611 10401 1278 550 21 1112 562
Error in data.frame(HOMSA.ENSEMBL = names(eg2ensembl), MUSMU.ENSEMBL = as.character(eg2ensembl)) : object 'eg2ensembl' not found`
It seems that in the celltype.R code, near line 1336, have some problem
} else if (id.type=="ENSEMBL") {
ensembl2ensembl <- idConverter(genome, srcSpecies="HOMSA", destSpecies="MUSMU", srcIDType="ENSEMBL", destIDType="ENSEMBL")
genome.mapping <- data.frame(HOMSA.ENSEMBL=names(eg2ensembl), MUSMU.ENSEMBL=as.character(eg2ensembl))
because eg2ensembl object does not exists and instead, ensembl2ensembl object exists.
Waiting for your response. Thank you