map_ids_annotationHub.Rdmap id Annotation Hub
map_ids_annotationHub( x, ID_col = "UniprotID", species = c("Homo sapiens", "Mus musculus") )
| x | data frame |
|---|---|
| ID_col | column with ID's |
| species | default "Homo sapiens" |
Other id_mapping:
map_ids_2ways(),
map_ids_uniprot(),
mapthe()
library(tidyverse) fc_estimates <- prora::exampleContrastData if (FALSE) { fc_estimates %>% filter(!(grepl("^REV_", protein_Id) | grepl("^zz", protein_Id) | grepl("^CON__", protein_Id))) } fc_estimates <- fc_estimates %>% filter(!(grepl("^REV_|^zz|^CON__", protein_Id))) filtered_dd <- get_UniprotID_from_fasta_header(fc_estimates, idcolumn = "protein_Id") dim(filtered_dd) #> [1] 3700 3 tmp <- map_ids_annotationHub(filtered_dd, species = "Homo sapiens") #> Warning: DEPRECATION: As of AnnotationHub (>2.23.2), default caching location has changed. #> Problematic cache: C:\Users\wolski\AppData\Local/AnnotationHub/AnnotationHub/Cache #> See https://bioconductor.org/packages/devel/bioc/vignettes/AnnotationHub/inst/doc/TroubleshootingTheCache.html#default-caching-location-update #> snapshotDate(): 2021-05-18 #> loading from cache #> 'select()' returned 1:many mapping between keys and columns sum(is.na(tmp$P_ENTREZGENEID )) #> [1] 20