[Bioc-sig-seq] GRanges, failure assigning chromosome lengths

[Ivan Gregoretti]

Hello listers,

Is anybody having trouble assigning seqlengths() to a GRanges instance
with the new GenomicRanges version?


This morning I upgraded my GenomicRanges from 0.0.9 to 0.1.17 and
since then I am unable to assign chromosome lengths to any of my tag
sets from my Illumina 36 nucleotide sequences.

On Friday this worked. Let me show you how it complains now:

Z <- import('millionsoftags.bed.gz', 'bed')

Z <- as(Z, 'GRanges')

class(Z)
[1] "GRanges"
attr(,"package")
[1] "GenomicRanges"

Z
GRanges with 23293177 ranges and 2 elementMetadata values
              seqnames               ranges strand   |
                 <Rle>            <IRanges>  <Rle>   |
       [1]        chr1   [3000506, 3000541]      +   |
       [2]        chr1   [3001061, 3001096]      -   |
       [3]        chr1   [3001075, 3001110]      -   |
       [4]        chr1   [3001098, 3001133]      +   |
       [5]        chr1   [3001310, 3001345]      +   |
       [6]        chr1   [3001559, 3001594]      +   |
       [7]        chr1   [3001603, 3001638]      +   |
       [8]        chr1   [3001603, 3001638]      +   |
       [9]        chr1   [3001609, 3001644]      -   |
       ...         ...                  ...    ... ...
[23293169] chrY_random [58402685, 58402720]      +   |
[23293170] chrY_random [58403358, 58403393]      +   |
[23293171] chrY_random [58406154, 58406189]      +   |
[23293172] chrY_random [58411077, 58411112]      -   |
[23293173] chrY_random [58430677, 58430712]      +   |
[23293174] chrY_random [58435117, 58435152]      -   |
[23293175] chrY_random [58472079, 58472114]      +   |
[23293176] chrY_random [58483725, 58483760]      -   |
[23293177] chrY_random [58487952, 58487987]      -   |
                                  name     score
                           <character> <numeric>
       [1]  HWI-EAS179_1:7:39:506:1302        96
       [2]  HWI-EAS179_1:2:69:562:1539       119
       [3]  HWI-EAS179_1:8:28:1327:394       119
       [4]   HWI-EAS179_1:7:96:619:454       119
       [5] HWI-EAS179_49:3:4:1219:1729       119
       [6]  HWI-EAS179_49:3:88:949:558       118
       [7] HWI-EAS179_1:7:60:1151:1790       119
       [8]  HWI-EAS179_1:7:61:1586:147       114
       [9]   HWI-EAS179_1:7:55:813:365       106
       ...                         ...       ...
[23293169] HWI-EAS179_1:7:49:1416:1573        17
[23293170]  HWI-EAS179_1:8:25:405:1723        59
[23293171] HWI-EAS179_1:7:75:1366:1224        25
[23293172]    HWI-EAS179_1:2:5:1338:80         5
[23293173]  HWI-EAS179_49:3:13:151:166        83
[23293174] HWI-EAS179_49:3:29:1091:472         6
[23293175]  HWI-EAS179_1:2:69:1424:733        17
[23293176]  HWI-EAS179_1:7:16:945:1051        25
[23293177] HWI-EAS179_1:7:74:1117:1801        14

seqlengths
         chr1        chr10        chr11 ...         chrY  chrY_random
           NA           NA           NA ...           NA           NA

# Here is the problem
seqlengths(Z) <- seqlengths(BSgenome)[names(seqlengths(Z))]
Error in function (classes, fdef, mtable)  :
  unable to find an inherited method for function "seqlengths", for
signature "function"

# Here is a second attempt that also fails
seqlengths(Z) <- seqlengths(Mmusculus)[names(seqlengths(Z))]
Error in validObject(.Object) :
  invalid class "GRanges" object: slot 'ranges' contains values
outside of sequence bounds


As you can see, I haven't had the chance to mess the data.
Any idea how to circumvent this problem?

Thank you,

Ivan


sessionInfo()
R version 2.12.0 Under development (unstable) (2010-03-25 r51410)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BSgenome.Mmusculus.UCSC.mm9_1.3.16 BSgenome_1.15.21
[3] Biostrings_2.15.27                 GenomicRanges_0.1.17
[5] IRanges_1.5.79                     rtracklayer_1.7.12
[7] RCurl_1.4-1                        bitops_1.0-4.1

loaded via a namespace (and not attached):
[1] Biobase_2.7.6 tools_2.12.0  XML_2.8-1


Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health