Remove an entire column from a data.frame in R

You can set it to NULL.

> Data$genome <- NULL
> head(Data)
   chr region
1 chr1    CDS
2 chr1   exon
3 chr1    CDS
4 chr1   exon
5 chr1    CDS
6 chr1   exon

As pointed out in the comments, here are some other possibilities:

Data[2] <- NULL    # Wojciech Sobala
Data[[2]] <- NULL  # same as above
Data <- Data[,-2]  # Ian Fellows
Data <- Data[-2]   # same as above

You can remove multiple columns via:

Data[1:2] <- list(NULL)  # Marek
Data[1:2] <- NULL        # does not work!

Be careful with matrix-subsetting though, as you can end up with a vector:

Data <- Data[,-(2:3)]             # vector
Data <- Data[,-(2:3),drop=FALSE]  # still a data.frame