Nothing
# Generate a folder of Wengo format annotation files from an excel input and a DB file
genAnnotationFiles <- function(fExcelName, colName="Uniprot",
DB.name = "pathwayDB.csv", folder="PWFiles", outFolder=tempdir()
)
{
sheets = names(loadWorkbook(fExcelName))
data.list = lapply(sheets, FUN=function(s){ readWorkbook(fExcelName, s) } )
id.list <- lapply(data.list, FUN=function(d){unique(d[,colName])})
# generate GO files
if ( !( folder %in% list.files(outFolder)) ) dir.create(file.path(outFolder,folder) )
# infer identifier type for Uniprot or Ensembl only!
IDS <- unique(unlist(id.list))
# Read in DB file
dat_db = read.csv(DB.name, stringsAsFactors=FALSE)
for (ii in seq_along(id.list) ) {
vvv <- unique(id.list[[ii]])
ANNOTID <- rep("", length(vvv))
ANNOTID[!is.na(match(vvv, dat_db[,1]))] <- dat_db[match(vvv, dat_db[,1], nomatch = 0),2]
res <- data.frame(vvv, ANNOTID)
names(res) <- c("Identifier", "ID")
write.table(res, file = paste0(outFolder,"/",folder,"/",sheets[ii],".txt"), sep = "\t", quote = FALSE,
row.names = FALSE, col.names = FALSE)
}
file.path(outFolder,folder)
}
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