[BioC] Rle factors, table and empty levels

[Valerie Obenchain]

Pete,

Thanks for the bug report. This is fixed in IRanges 1.17.11.

Note that the data inside the rle must be a factor. Adding levels to an 
Rle after the fact doesn't create a factor-Rle.

x = Rle(c(2,3,1,2,3,2),rep(2,6))
levels(x) = as.character(0:5)

This is a numeric-Rle with no levels.

 > x
numeric-Rle of length 12 with 6 runs
   Lengths: 2 2 2 2 2 2
   Values : 2 3 1 2 3 2

 > table(x)

1 2 3
2 6 4

The same is true for a numeric vector. table() on a non-factor argument 
will drop unused levels.
v <- rep(c(2,3,1,2,3,2), each=2)
levels(v) <- 0:5
 > table(v)
v
1 2 3
2 6 4


If we create a factor-Rle, table() will retain all levels.

x_f = Rle(factor(rep(c(2,3,1,2,3,2), each=2), levels=0:5))
 > x_f
factor-Rle of length 12 with 6 runs
   Lengths: 2 2 2 2 2 2
   Values : 2 3 1 2 3 2
Levels(6): 0 1 2 3 4 5

 > table(x_f)

0 1 2 3 4 5
0 2 6 4 0 0


Valerie

On 10/29/2012 08:13 PM, Valerie Obenchain wrote:
> Thanks Pete. I'll look into it.
>
> Valerie
>
> On 10/29/12 14:28, Peter Haverty wrote:
>> Dear Group,
>>
>> table(Rle) seems to ignore empty levels.
>>
>> x = Rle(c(2,3,1,2,3,2),rep(2,6))
>> levels(x) = as.character(0:5)
>> table(x)
>> table(factor(as.numeric(x),levels=as.character(0:5)))
>>
>> I am using R 2.15.1 and IRanges 1.17.1.
>>
>> Regards,
>> Pete
>>
>> ____________________
>> Peter M. Haverty, Ph.D.
>> Genentech, Inc.
>> phaverty at gene.com
>>
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