[Bioc-sig-seq] GRanges resize Behaviour

[Dario Strbenac]

Hi,

I'd like to point out that resize extends beyond the start of a chromosome, for reads that are close to the start, and on the negative strand.

> gr
GRanges with 1 range and 0 elementMetadata values
    seqnames     ranges strand |
       <Rle>  <IRanges>  <Rle> |
[1]     chr2 [250, 285]      - |

> resize(gr, 300)
GRanges with 1 range and 0 elementMetadata values
    seqnames     ranges strand |
       <Rle>  <IRanges>  <Rle> |
[1]     chr2 [-14, 285]      - |

seqlengths
 chr2
   NA

Would the desirable behaviour be to only extend to base 1 ?

One more question. In the user manual (page 12, bottom), it says lapply can be used on a GRangesList, but it's not working for me.

> grl
GRangesList of length 3
$gr1 
GRanges with 1 range and 2 elementMetadata values
    seqnames    ranges strand |     score        GC
       <Rle> <IRanges>  <Rle> | <integer> <numeric>
[1]     chr2    [3, 6]      + |         5      0.45

$gr2 
GRanges with 2 ranges and 2 elementMetadata values
    seqnames    ranges strand |     score        GC
       <Rle> <IRanges>  <Rle> | <integer> <numeric>
[1]     chr1  [ 7,  9]      + |         3       0.3
[2]     chr1  [13, 15]      - |         4       0.5

$gr3 
GRanges with 2 ranges and 2 elementMetadata values
    seqnames    ranges strand |     score        GC
       <Rle> <IRanges>  <Rle> | <integer> <numeric>
[1]     chr1    [1, 3]      - |         6       0.4
[2]     chr2    [4, 9]      - |         2       0.1


seqlengths
 chr2 chr1
   NA   NA

> lapply(grl, cat, "Hello")
Error in as.list.default(X) : 
  no method for coercing this S4 class to a vector

--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia