 Dear bioc-sig-sequencing,

I would like to annotate chip-seq peaks for the arabidopsis genome.  In trying to work thru the GenomicFeatures vignette dated 03/27/10, I need to apply 'findOverlaps' to learn which chipseq peaks will overlap with Arabidopsis transcrips.  However, I get the following error. Perhaps I need to use the 'sub' function to change the values in the 'seqnames' column in either 'GR_txdb' or 'r_gr_ChSeqPks'? Could someone recommend what I should try?


> mart4_at_eg_gene
TranscriptDb object:
| Db type: TranscriptDb
| Data source: BioMart
| BioMart database: plant_mart_4
| BioMart dataset: athaliana_eg_gene
| BioMart dataset description: Arabidopsis thaliana genes (TAIR9)
| BioMart dataset version: TAIR9
| Full dataset: yes
| transcript_nrow: 39640
| exon_nrow: 176581
| cds_nrow: 0
| Db created by: GenomicFeatures package from Bioconductor
| Creation time: 2010-04-01 11:11:41 -0500 (Thu, 01 Apr 2010)
| GenomicFeatures version at creation time: 0.5.0
| RSQLite version at creation time: 0.8-4

> rd0_chr1_s_8_trt_vs_INPctl[["strand"]] = "*"
> gr_ChSeqPks <- as(rd0_chr1_s_8_trt_vs_INPctl, "GRanges")
> gr_ChSeqPks
GRanges with 57 ranges and 2 elementMetadata values
     seqnames               ranges strand   |     ARAB8 ARAB7INPCTL
        <Rle>            <IRanges>  <Rle>   | <integer>   <integer>
 [1]     chr1   [ 617092,  617094]      *   |        24           0
 [2]     chr1   [1808262, 1808262]      *   |         8           0
 [3]     chr1   [3889445, 3889452]      *   |        64           0
 [4]     chr1   [4404410, 4404410]      *   |         8           0
 [5]     chr1   [7081127, 7081127]      *   |         8           0
 [6]     chr1   [7128574, 7128581]      *   |        64           0
...

> GR_txdb <- transcripts(mart4_at_eg_gene)
> GR_txdb
GRanges with 39640 ranges and 2 elementMetadata values
        seqnames           ranges strand   |     tx_id          tx_name
           <Rle>        <IRanges>  <Rle>   | <integer>      <character>
    [1]        1   [ 3631,  5899]      +   |      5480 AT1G01010.1-TAIR
    [2]        1   [23146, 31227]      +   |      3216 AT1G01040.1-TAIR
    [3]        1   [28500, 28706]      +   |      8461 AT1G01046.1-TAIR
    [4]        1   [44677, 44787]      +   |      3566 AT1G01073.1-TAIR
    [5]        1   [52239, 54692]      +   |      7451 AT1G01110.2-TAIR
    [6]        1   [52869, 54685]      +   |      7450 AT1G01110.1-TAIR
...
seqlengths
 1  2  3  4  5 Pt Mt
NA NA NA NA NA NA NA

> r_gr_ChSeqPks <- reduce(gr_ChSeqPks)
> OL <- findOverlaps(GR_txdb, r_gr_ChSeqPks)
Error in .local(query, subject, maxgap, minoverlap, type, select, ...) :
  'query' and 'subject' do not use a similiar naming convention for seqnames

> sessionInfo()
R version 2.12.0 Under development (unstable) (2010-03-30 r51506)
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] biomaRt_2.3.5         GenomicFeatures_0.5.0 GenomicRanges_0.1.0
[4] IRanges_1.5.73

loaded via a namespace (and not attached):
[1] Biobase_2.7.5      Biostrings_2.15.26 BSgenome_1.15.20   DBI_0.2-5
[5] RCurl_1.3-1        RSQLite_0.8-4      rtracklayer_1.7.11 tools_2.12.0
[9] XML_2.8-1
>


Thanks,
P. Terry
pterry@huskers.unl.edu

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