How to convert gene IDs to gene symbols in R?

Question

[Amr]

I am performing PCA in R and I got top 10 measurements (genes) that contribute for PC1:

loading_scores <- pca$rotation[,1]
gene_scores <- abs(loading_scores) ## get the magnitudes
gene_score_ranked <- sort(gene_scores, decreasing=TRUE)
top_10_genes <- names(gene_score_ranked[1:10])
top_10_genes

output:

 [1] "ENSG00000169018.5"  "ENSG00000181038.13" "ENSG00000103275.18" "ENSG00000174796.12"
 [5] "ENSG00000164087.7"  

How can I convert the ouputs from "gene IDs" into gene symbols? so that the outputs be like:

FEM1B

METTL23

UBE2I

etc..

Thanks in advance

[cpad0112]

for humans, use org.hs.eg.db

[Amr]

yes for humans, but how?

Answer 1

[Kevin Blighe]

Hello, please check my answer, here: Translating gene names to entrez id's

Note that you will need to remove those numerical suffixes from the Ensembl gene IDs

[Amr]

I run the first command:

library(org.Hs.eg.db)
mapIds(
  org.Hs.eg.db,
  keys = genes,
  column = 'ENTREZID',
  keytype = 'SYMBOL')
select(
  org.Hs.eg.db,
  keys = genes,
  column = c('SYMBOL', 'ENTREZID', 'ENSEMBL'),
  keytype = 'SYMBOL')

But I still cant convert the extracted genesIDs to the symbols? How related to that code? Where I should put top_10_genes?

Thanks for answering

[Kevin Blighe]

require(org.Hs.eg.db)

mapIds(
  org.Hs.eg.db,
  keys = genes,
  column = 'SYMBOL',
  keytype = 'ENSEMBL')

select(
  org.Hs.eg.db,
  keys = genes,
  column = c('SYMBOL', 'ENTREZID', 'ENSEMBL'),
  keytype = 'ENSEMBL')

[Amr]

How related to that code? Where I should put top_10_genes?

[Kevin Blighe]

I have provided enough information such that you should be able to adapt my code to your own code. Please review my answer via the other link, to help you understand.

[cpad0112]

keys = top_10_genes