after
library(GenomicFeatures)
example(GRanges)
you can experiment with the object gr
> levels(seqnames(gr))
[1] "Chrom1" "Chrom2" "Chrom3"
> levels(seqnames(gr)) = as.character(1:3)
> levels(seqnames(gr))
[1] "1" "2" "3"
> gr
GRanges with 10 ranges and 2 elementMetadata columns
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
a 1 [ 1, 10] - | 1 1.0000000
b 2 [ 2, 10] + | 2 0.8888889
c 2 [ 3, 10] + | 3 0.7777778
d 2 [ 4, 10] * | 4 0.6666667
e 1 [ 5, 10] * | 5 0.5555556
f 1 [ 6, 10] + | 6 0.4444444
g 3 [ 7, 10] + | 7 0.3333333
h 3 [ 8, 10] + | 8 0.2222222
i 3 [ 9, 10] - | 9 0.1111111
j 3 [10, 10] - | 10 0.0000000
resetting the levels as above is one way to harmonize seqnames for your
problem
On Fri, Apr 2, 2010 at 12:05 AM, [email protected] <
[email protected]> wrote:
> 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
> [email protected]
>
> [[alternative HTML version deleted]]
>
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>
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