search

NathanSkene / EWCE

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.
https://nathanskene.github.io/EWCE/index.html
53 stars 25 forks source link

fix HGNC names exits with error #2

Closed rbutleriii closed 3 years ago

rbutleriii commented 5 years ago

Running the fix hgnc script errors out.

> fix.bad.hgnc.symbols(ctd_darmanis, dropNonHGNC = F)
[1] "2841 of 22088 are not proper HGNC symbols"
[1] "Possible corruption of gene names by excel: SEP15, SEPN1, SEPP1, SEPT5-GP1BB, SEPT7L, SEPW1, SEPX1"
[1] "1597 of 22088 gene symbols corrected"
[1] "1365 of 22088 gene symbols cannot be mapped"
           astrocytes-GSM1657885 astrocytes-GSM1657932 astrocytes-GSM1657938 astrocytes-GSM1657965
SEC24B-AS1                     0                     0                     0                     0
A1BG                           0                     0                     0                     0
A1BG-AS1                       0                     0                     0                     0
.
.
.
Warning messages:
1: In fix.bad.hgnc.symbols(ctd_darmanis, dropNonHGNC = F) :
  Possible corruption of gene names by excel: SEP15, SEPN1, SEPP1, SEPT5-GP1BB, SEPT7L, SEPW1, SEPX1
2: In checkGeneSymbols(rownames(exp_CORRECTED), unmapped.as.na = TRUE) :
  Some lower-case letters were found and converted to upper-case.
                 HGNChelper is intended for human symbols only, which should be all
                 upper-case except for open reading frames (orf).
3: In checkGeneSymbols(rownames(exp_CORRECTED), unmapped.as.na = TRUE) :
  x contains non-approved gene symbols
4: In checkGeneSymbols(rownames(exp_CORRECTED), unmapped.as.na = FALSE) :
  Some lower-case letters were found and converted to upper-case.
                 HGNChelper is intended for human symbols only, which should be all
                 upper-case except for open reading frames (orf).
5: In checkGeneSymbols(rownames(exp_CORRECTED), unmapped.as.na = FALSE) :
  x contains non-approved gene symbols
NathanSkene commented 3 years ago

I'm a bit late replying to this. Guessing you've not got the relevant files left for reproducing this. Can't actually see the error, those are warnings, figured it was better if there are warnings when genes are renamed as it may not be the desired behaviour. Closing it now as I can't see how to proceed.