tximeta accessing gene symbols after addIds()
Entering edit mode
7 weeks ago
iddryg • 0

Hi, I'm sure I'm missing something obvious, but is there an easy way to access the gene symbols after adding them with the addIds() function in tximeta?

gse <- addIds(gse, "SYMBOL", gene=TRUE)
DataFrame with 60240 rows and 3 columns
ENSG00000000003.15 ENSG00000000003.15
ENSG00000000005.6   ENSG00000000005.6
ENSG00000000419.12 ENSG00000000419.12
ENSG00000000457.14 ENSG00000000457.14
ENSG00000000460.17 ENSG00000000460.17
...                               ...
ENSG00000288600.1   ENSG00000288600.1
ENSG00000288601.1   ENSG00000288601.1
ENSG00000288602.1   ENSG00000288602.1
ENSG00000288603.1   ENSG00000288603.1
ENSG00000288604.1   ENSG00000288604.1
ENSG00000000003.15  ENST00000373020.9,ENST00000612152.4,ENST00000614008.4,...
ENSG00000000005.6                         ENST00000373031.5,ENST00000485971.1
ENSG00000000419.12  ENST00000371588.9,ENST00000466152.5,ENST00000371582.8,...
ENSG00000000457.14 ENST00000367771.11,ENST00000367770.5,ENST00000367772.8,...
ENSG00000000460.17  ENST00000498289.5,ENST00000472795.5,ENST00000359326.9,...
...                                                                       ...
ENSG00000288600.1                                           ENST00000674216.1
ENSG00000288601.1                                           ENST00000674448.1
ENSG00000288602.1                         ENST00000520044.5,ENST00000519289.1
ENSG00000288603.1                                           ENST00000674332.1
ENSG00000288604.1                                           ENST00000674461.1
ENSG00000000003.15       TSPAN6
ENSG00000000005.6          TNMD
ENSG00000000419.12         DPM1
ENSG00000000457.14        SCYL3
ENSG00000000460.17     C1orf112
...                         ...
ENSG00000288600.1            NA
ENSG00000288601.1     RNA5SP424
ENSG00000288602.1  C8orf44-SGK3
ENSG00000288603.1    SNORA74C-2
ENSG00000288604.1            NA

So I know that the gene symbols are in there somewhere, but I'm not sure how to access them. Later when doing differential expression with deseq2, it still shows the ensembl gene ids and not the symbols.

res_test %>% head(3)
log2 fold change (MLE): Serum 10_perc_FCS vs 2_perc_FCS 
Wald test p-value: Serum 10_perc_FCS vs 2_perc_FCS 
DataFrame with 3 rows and 6 columns
                    baseMean log2FoldChange     lfcSE      stat    pvalue
                   <numeric>      <numeric> <numeric> <numeric> <numeric>
ENSG00000000003.15   423.607       0.317025  0.170508   1.85930 0.0629842
ENSG00000000005.6      0.000             NA        NA        NA        NA
ENSG00000000419.12   532.836       0.356938  0.148210   2.40834 0.0160254
ENSG00000000003.15  0.241174
ENSG00000000005.6         NA
ENSG00000000419.12  0.099506

Any way to pull those gene symbols out and replace the ensembl ids? I know there are other ways to do this more manually like with org.Hs.eg.db but I feel like I'm just missing a simple function here. Thanks!

deseq2 symbols tximeta gene • 172 views

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