Deleted:How to retrieve Entrez IDs using Gene Symbols?
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Melissa • 0
@161a251e
Last seen 7 days ago
Malaysia

I want to replace the index of the dataframe (Gene Symbols) with GENE_ID:GENE_VALUE to use as a data matrix input for netgsa R package (https://cran.r-project.org/web/packages/netgsa/vignettes/netgsa.html).

First, I retrieve the Entrez IDs:

library(org.Hs.eg.db)
library(AnnotationDbi)

# gene_value is the Entrez ID
gene_value = mapIds(org.Hs.eg.db, keys=rownames(meth_df), column="ENTREZID", keytype="SYMBOL")

Traceback:

'select()' returned 1:many mapping between keys and columns

Then, I want to append the string ENTREZID: to the gene_value variable.

rownames(meth_df) <- paste0("ENTREZID:", gene_value)

Expected rownames output (example):

## [1] "ENTREZID:127550" "ENTREZID:53947"  "ENTREZID:65985"  "ENTREZID:51166" 
## [5] "ENTREZID:15"     "ENTREZID:60496"

Example data:

> dput(meth_df[1:5,1:5])
structure(list(`TCGA-2K-A9WE-01A` = c(0.611033076810465, 0.786837244239289, 
0.531054614303851, 0.711916183761331, 0.758443223998425), `TCGA-2Z-A9J1-01A` = c(0.468013052647261, 
0.386177267500376, 0.508623627469028, 0.403601275088479, 0.754642399207848
), `TCGA-2Z-A9J2-01A` = c(0.593559707995411, 0.54983504208745, 
0.535207192925841, 0.613971903755576, 0.717278085189431), `TCGA-2Z-A9J3-01A` = c(0.638211007873003, 
0.319561448644096, 0.526699541432941, 0.450002172806716, 0.736440001203422
), `TCGA-2Z-A9J5-01A` = c(0.603998109440889, 0.638039512259872, 
0.584328151056768, 0.594021097192165, 0.818583455926719)), row.names = c("A1BG", 
"A1CF", "A2BP1", "A2LD1", "A2M"), class = "data.frame")
AnnotationDbi • 37 views
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