How to replace Gene Symbols with Ensembl ID?

Question

[melissachua90]

I want to replace the gene_symbols of my data frame with the Ensembl ID.

library(biomaRt)

genes <- rownames(exp.kirp)

ensembl <- useMart("ensembl", dataset="hsapiens_gene_ensembl")

g_list <- getBM(attributes = c('ensembl_gene_id','hgnc_symbol', 
                               filters='hgnc_symbol',values=genes,
                               mart=ensembl))

Traceback:

Error in martCheck(mart) : 
  You must provide a valid Mart object. To create a Mart object use the function: useMart.  Check ?useMart for more information.

Sample data:

> dput(exp.kirp[1:10,1:10])
structure(list(TCGA.2K.A9WE.01A = c(201.3304, 4.1094, 0.5137, 
81.9109, 0, 20899.5608, 1326.8268, 13.8693, 0, 1083.8577), TCGA.2Z.A9J1.01A = c(34.1519, 
37.1701, 0, 122.4433, 0, 5456.0922, 2339.2393, 7.9296, 0, 1169.124
), TCGA.2Z.A9J2.01A = c(45.8403, 17.345, 0, 184.9223, 0, 4954.3084, 
976.2745, 0, 0, 1277.3338), TCGA.2Z.A9J3.01A = c(26.0224, 10.1339, 
11.9435, 187.0069, 0, 1151.2088, 1001.8096, 39.0879, 0, 937.7488
), TCGA.2Z.A9J5.01A = c(255.3725, 36.8627, 3.1373, 118.8157, 
0, 13154.1333, 1324.7059, 6.2745, 0, 1367.8431), TCGA.2Z.A9J6.01A = c(35.1924, 
99.4503, 0.4998, 121.8191, 0, 4201.5892, 1808.096, 45.4773, 0, 
1283.8581), TCGA.2Z.A9J7.01A = c(123.7406, 4.755, 0, 152.2335, 
2.1133, 1999.8732, 1551.1821, 20.0766, 0, 1404.3059), TCGA.2Z.A9J8.01A = c(12.2705, 
42.0701, 0, 242.3773, 0.3339, 4089.1853, 964.6077, 34.3907, 0, 
995.9933), TCGA.2Z.A9J9.01A = c(66.4361, 0.374, 0, 53.1638, 0.374, 
29835.2992, 1418.1002, 22.8123, 0.7479, 624.1586), TCGA.2Z.A9JD.01A = c(8.916, 
19.1909, 0, 407.1369, 0, 1979.1183, 1784.751, 2.5934, 0, 729.2531
)), row.names = c("A1BG", "A1CF", "A2BP1", "A2LD1", "A2ML1", 
"A2M", "A4GALT", "A4GNT", "AAA1", "AAAS"), class = "data.frame")

[LChart]

What is the error message that appears after ensembl <- useMart("ensembl", dataset="hsapiens_gene_ensembl"); the ensembl variable isn't being set, so there has to be an error.

Answer 1

[nhaus]

You closed the bracket at the wrong position. This code should do what you want:

ensembl = useEnsembl(
  biomart = "genes",
  dataset = "hsapiens_gene_ensembl",
  GRCh = 37,
  verbose = T
)

ensembl <- useDataset(dataset = "hsapiens_gene_ensembl", mart = ensembl)

g_list <- getBM(attributes = c('ensembl_gene_id','hgnc_symbol'), 
                               filters='hgnc_symbol',values=your_genes,
                               mart=ensembl)