I installed package EnsDb.Hsapiens.v86 to convert genes ensembl to symbol, after trying many packages that's the best one to conversion with less NAs. I tried to write the code but I got unsual error, here's my code:
library(EnsDb.Hsapiens.v86)
mapIds = mapIds (EnsDb.Hsapiens.v86,
keys = genes,
keytype = "GENEID",
column = "SYMBOL")
after that code conversion must be done, but I got this error:
Error: 'filter' has to be an 'AnnotationFilter', a list of 'AnnotationFilter' object, an 'AnnotationFilterList' or a valid filter expression!
CodePudding user response:
Maybe your keys are problematic, e.g. not a character vector. Try if it works for you with the reproducible example below:
library(EnsDb.Hsapiens.v86)
genes <- c("ENSG00000102145", "ENSG00000179348", "ENSG00000107485")
mapIds(EnsDb.Hsapiens.v86,
keys = genes,
keytype = "GENEID",
column = "SYMBOL")
#> ENSG00000102145 ENSG00000179348 ENSG00000107485
#> "GATA1" "GATA2" "GATA3"
Created on 2022-04-10 by the reprex package (v2.0.1)