I had a GRanges object that I converted to a data frame. I am then sorting it by chr and start position:
df[order(df$seqnames, df$start),]
However, the resulting data frame starts with chr17. All chromosomes are present, including chr1 and chr10, which should come up before chr17. Is there some additional metadata that I am not aware of?
I'm guessing that the levels of the factor are in the wrong order. This should come directly from the order of the seqlevels in your original GRanges. You can fix your seqlevels automatically using sortSeqlevels(). Btw, sorting the GRanges before conversion to data.frame might be easier, since it is basically just sort(gr), but you will need to fix their order first.
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version 2.3.6
I forgot that factors have their own order. I converted seqnames to characters. I think that's even easier.
Perhaps. But you lose the information that the factor provides. For example, if you plot the data by chromosome, they will likely be rendered in a non-natural order.