Hello,

I have some points according to the internal order of granges objects.

1) Automatically there is an order depending on the a) seqnames (=
chromosomes) and b) the ranges.

2) The seqnames are always sorted in ascii order.

3) After
    df <- as.data.frame
    m <- regexpr ("\\d+", df$seqnames, perl=TRUE)
    df$Chromosome <- regmatches (df$seqnames, m)
    df$Chromosome <- as.integer (as.character (df$Chromosome))
    df <- df [order(df$Chromosome),]
    only the order of the chromosomes is changed. The order of the ranges
(now df$start and df$end) is still the same.

Are my assumptions true?

Thanks Hermann

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