transId() updating symbols weird behaviour

[MEladawi]

Hello--

I am updating old gene symbols with keepNA = FALSE, unique = FALSE.

I am getting some strange data (please see below). row 138 (Gm553): is official symbol and it is returned as NA. row 149-151: the original symbols are Ankrd44 & 4930444A19Rik. row 156 & 157 (Mob4): it comes one time as Mob4 and one time as NA.

[reedliu]

The gene name is a little tidious thing. For example,

• For gene Gm553 (Mouse Gene, Strain: C3H/HeJ), you could see it is based on strain genomes such as MGP_C3HHeJ and MGP_C57BL6NJ. While the transId function now only give results based on standard genome like GRCm39. So does gene Mob4.

• 4930444A19Rik has own records (ENSMUSG00000101674 and 73980 for NCBI, https://www.ncbi.nlm.nih.gov/gene/73980), while it is also the gene alias of Ankrd44 (329154 for NCBI, https://www.ncbi.nlm.nih.gov/gene/329154)

If you want to get one-to-one match, please set "unique=TRUE" and it will return you the best-matching one. (I have given the function some rules to get the best-matching one, while it is a long story...)

[MEladawi]

Thanks! This makes sense..