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error in celltype.enrichment function with id.type="ENSEMBL" + species="HOMSA" #8

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LovelessOne opened this issue Jul 31, 2018 · 0 comments

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@LovelessOne
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LovelessOne commented Jul 31, 2018

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

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