Based on your comments, you wish to obtain a semi-colon separated list of unique values in the gene column. You can create a new column containing these using:

```r
xyz <- data.frame(chr="chr1", gene = c("RUNX3;RUNX3", "RUNX3;RUNX3", "SFN", "NR0B2", "NR0B2", "TFAP2E", "A;B;A"))

xyz
   chr        gene
1 chr1 RUNX3;RUNX3
2 chr1 RUNX3;RUNX3
3 chr1         SFN
4 chr1       NR0B2
5 chr1       NR0B2
6 chr1      TFAP2E
7 chr1       A;B;A

xyz$gene_uniq <- sapply(xyz$gene, function(x) paste(unique(unlist(strsplit(x, ";"))), collapse=";"))

xyz
   chr        gene gene_uniq
1 chr1 RUNX3;RUNX3     RUNX3
2 chr1 RUNX3;RUNX3     RUNX3
3 chr1         SFN       SFN
4 chr1       NR0B2     NR0B2
5 chr1       NR0B2     NR0B2
6 chr1      TFAP2E    TFAP2E
7 chr1       A;B;A       A;B
```

Or you can use dplyr. I'll edit and paste an example below.