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travis.m.couture
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@travismcouture-10788
Last seen 7.9 years ago
Hey everyone. When I run the following code it raises an error:
me3.p10 <- pileup(position(foo), width(foo), seqlens[["10"]]) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘pileup’ for signature ‘"integer"’
For background on my data and purpose, follow this guide: http://www.bioconductor.org/packages/2.4/bioc/vignettes/ShortRead/inst/doc/ShortRead_and_HilbertVis.pdf
I am essentially trying to learn HilbertVis to plot some genomic data I have. Thanks for your help in advance!
Additional Info:
Link to all source data: http://www.ebi.ac.uk/~anders/ShortReadExampleData/
Code used:
library("ShortRead")
> maps.me1 <- sapply( list.files( "H3K4me1", "run.*lane.\\.map" ),
function(filename) readAligned( "H3K4me1", filename, type="MAQMapShort" ) )
> maps.me3 <- sapply( list.files( "H3K4me3", "run.*lane.\\.map" ),
function(filename) readAligned( "H3K4me3", filename, type="MAQMapShort" ) )
> seqlens <- c( `10`=135374737, `11`=134452384, `12`=132349534,
`13`=114142980, + `14`=106368585, `15`=100338915, `16`=88827254,
`17`=78774742, `18`=76117153, `19`=63811651, `1`=247249719,
`20`=62435964, `21`=46944323, `22`=49691432, `2`=242951149,
`3`=199501827, `4`=191273063, `5`=180857866, `6`=170899992,
`7`=158821424, `8`=146274826, `9`=140273252, MT=16571, X=154913754,
Y=57772954 )
> foo <- maps.me3$run13_lane4.map[
chromosome( maps.me3$run13_lane4.map ) == "10" &
quality(alignQuality( maps.me3$run13_lane4.map )) >= 15
> me3.p10 <- pileup( position(foo), width(foo), seqlens[["10"]] )
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘pileup’ for signature ‘"integer"’
sessioninfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: CentOS release 6.7 (Final)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] ShortRead_1.28.0 GenomicAlignments_1.6.3 SummarizedExperiment_1.0.2 Biobase_2.30.0 Rsamtools_1.24.0
[6] GenomicRanges_1.22.4 GenomeInfoDb_1.6.3 Biostrings_2.38.4 XVector_0.10.0 IRanges_2.4.7
[11] S4Vectors_0.8.11 BiocParallel_1.4.3 BiocGenerics_0.16.1 HilbertVis_1.30.0 lattice_0.20-33
loaded via a namespace (and not attached):
[1] bitops_1.0-6 futile.options_1.0.0 zlibbioc_1.16.0 hwriter_1.3.2 latticeExtra_0.6-28 futile.logger_1.4.1 RColorBrewer_1.1-2
[8] lambda.r_1.1.7 tools_3.2.0
You are being unnecessarily vague. The reason the posting guide says to give a self-contained example is because questions like yours are the equivalent of saying "I did something and it didn't work". Unless you give an example that anybody else can use to reproduce the error, nobody can help you.
I gave a link to the guide which contains the sample data I am using as well as all the specific commands I used. I can copy and past everything to my post...
I've added your additional info to the original question, and will remove it from below.