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AddGOGeneList.manual() used, but now only part of Gruffi's source code #10

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vertesy opened this issue Feb 1, 2022 · 1 comment
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@vertesy
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vertesy commented Feb 1, 2022

Description
AddGOGeneList.manual() missing in if (TRUE) source('~/GitHub/Packages/Seurat.pipeline/elements/Differential.gene.expression.Loop.R'); create_set_Original_OutDir()

AddGOGeneList.manual <- function(obj = combined.obj, GO = 'GO:0034976'  # Add GO terms via Biomart package
                                 , genes =  c("A0A140VKG3", "ARX", "CNTN2", "DRD1", "DRD2", "FEZF2", "LHX6")) {
  genes <- IntersectWithExpressed(obj = obj, genes = genes)

  if (is.null(obj@misc$GO)) obj@misc$GO <- list()
  obj@misc$GO[[make.names(GO)]] <- genes
  iprint("Genes in", GO, "are saved under obj@misc$GO$", make.names(GO))
  if (web.open) system(paste0("open https://www.ebi.ac.uk/QuickGO/search/", GO))
  return(obj)
}
@vertesy vertesy added the bug Something isn't working label Feb 1, 2022
@vertesy
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vertesy commented Aug 8, 2022

Well, gruffi::AddGOGeneList.manual

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