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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")