inst/develo/ensg2symbol.R

In C3BI-pasteur-fr/UTechSCB-SCHNAPPs: Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data

fps <- list.files(
  pattern = ".RData$|.RDs$",
  path = "~/Downloads/",
  recursive = TRUE,
  full.names = T,
  ignore.case = T
)
for (fp in fps) {
  print(fp)
  cont <- T
  scEx <- NULL
  cp <- tryCatch(load(file = fp),
    error = function(x) {
      # print(x)
      cont <- F
    }
  )
  if (cont) {
    if (is.null(scEx)) {
      print(paste(fp, "no scEX"))
    } else {
      if (startsWith(rownames(scEx)[1], "ENS")) {
        if ("symbol" %in% colnames(rowData(scEx))) {
          print(head(rownames(scEx)))
          rownames(scEx) <- make.unique(rowData(scEx)$symbol)
          save(file = paste0(fp, ".noENSG.RData"), list = c("scEx"))
        }
      }
    }
  }
}

rownames(scEx) <- make.unique(rowData(scEx)$symbol)