Entering edit mode
> James W. MacDonald <jmacdon at="" ...=""> writes:
> You would be better off using the FDb.InfiniumMethylation.hg19
package,
> which not only has all the locations for the probes, but also has
them
> in a more useful format.
>
> > library(FDb.InfiniumMethylation.hg19)
> > x <- get450k()
> Warning message:
> In if is.na(genome(GR))) { :
> the condition has length > 1 and only the first element will be
used
> > x
> GRanges with 485577 ranges and 7 metadata columns:
> seqnames ranges strand | addressA
addressB
> channel
> <rle> <iranges> <rle> | <rle> <rle> <rle>
> cg13869341 chr1 [15865, 15866] * | 62703328
> 16661461 Red
> cg14008030 chr1 [18827, 18828] * | 27651330 <na>
Both
> cg12045430 chr1 [29407, 29408] * | 25703424
> 34666387 Red
> cg20826792 chr1 [29425, 29426] * | 61731400
> 14693326 Red
> cg00381604 chr1 [29435, 29436] * | 26752380
> 50693408 Red
Does anyone know why Jim's lines of code do not work on my R
installation
(R3.0.1)?
Many thanks,
Ed
library(FDb.InfiniumMethylation.hg19)
x <- get450k()
Error in `seqinfo<-`(`*tmp*`, value = NULL) :
the supplied 'seqinfo' must be a Seqinfo object
In addition: Warning message:
In if is.na(genome(GR))) { :
the condition has length > 1 and only the first element will be used
sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C
LC_COLLATE=C LC_MONETARY=C
[6] LC_MESSAGES=C LC_PAPER=C LC_NAME=C
LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets
methods
base
other attached packages:
[1] IlluminaHumanMethylation450k.db_2.0.7 org.Hs.eg.db_2.9.0
[3] RSQLite_0.11.4 DBI_0.2-7
[5] FDb.InfiniumMethylation.hg19_1.0.1 rtracklayer_1.20.2
[7] GenomicFeatures_1.12.2 AnnotationDbi_1.22.6
[9] BiocInstaller_1.10.2 minfi_1.6.0
[11] Biostrings_2.28.0 GenomicRanges_1.12.4
[13] IRanges_1.18.1 reshape_0.8.4
[15] plyr_1.8 lattice_0.20-15
[17] Biobase_2.20.1 BiocGenerics_0.6.0
loaded via a namespace (and not attached):
[1] BSgenome_1.28.0 MASS_7.3-26 R.methodsS3_1.4.4
RColorBrewer_1.0-5 RCurl_1.95-4.1
[6] Rsamtools_1.12.3 XML_3.98-1.1 beanplot_1.1
biomaRt_2.16.0 bitops_1.0-5
[11] grid_3.0.1 illuminaio_0.2.0 limma_3.16.5
matrixStats_0.8.1 mclust_4.1
[16] multtest_2.16.0 nor1mix_1.1-4 preprocessCore_1.22.0
siggenes_1.34.0 splines_3.0.1
[21] stats4_3.0.1 survival_2.37-4 tools_3.0.1
zlibbioc_1.6.0
