[BioC] methyAnalysis for DMR identification
Allegra Petti [guest]
guest at bioconductor.org
Mon Feb 24 23:52:58 CET 2014
Hello,
I was wondering if anyone here has tried methyAnalysis for identifying Differentially Methylated Regions in Illumina 450k array data. It seems to have wonderful data-visualization options, but it found no differentially-methylated regions in my data (56 450k data sets), which was surprising. I've found very little documentation for this method, and I am wondering if I did something wrong - for example, should I have performed the smoothMethyData function separately, with a different window size? Relevant code snippets and output are provided below. I'd greatly appreciate any thoughts or suggestions.
Thank you very much!
Allegra
__________________________________________________________
Code:
library(lumi);
library(methylumi);
library(wateRmelon);
library(methyAnalysis);
library(IlluminaHumanMethylation450k.db);
library(IlluminaHumanMethylation450kanno.ilmn12.hg19); # Note: had to be installed manually
barcodes <- readLines("barcodes.txt"); # read barcodes from a text file
classes <- readLines("IdatClasses.txt");
data.s <- methylumIDAT(barcodes); # read in idat files (methylumi function)
*** additional data processing ***
data.m <- as(data.s, "MethyLumiM"); # convert to MethyLumiM object
data.g <- MethyLumiM2GenoSet(data.m, lib = "IlluminaHumanMethylation450k.db"); # convert MethyLumiM to MethyGenoSet
dmrResult <- detectDMR.slideWin(data.g, sampleType=classes); # smooth data and find DMRs
allDMRInfo <- identifySigDMR(dmrResult);
___________________________________________________________________
Standard Output:
65 probes were removed because of lack of chromosome location information!
Smoothing Chromosome chr1 ...
Smoothing Chromosome chr10 ...
Smoothing Chromosome chr11 ...
Smoothing Chromosome chr12 ...
Smoothing Chromosome chr13 ...
Smoothing Chromosome chr14 ...
Smoothing Chromosome chr15 ...
Smoothing Chromosome chr16 ...
Smoothing Chromosome chr17 ...
Smoothing Chromosome chr18 ...
Smoothing Chromosome chr19 ...
Smoothing Chromosome chr2 ...
Smoothing Chromosome chr20 ...
Smoothing Chromosome chr21 ...
Smoothing Chromosome chr22 ...
Smoothing Chromosome chr3 ...
Smoothing Chromosome chr4 ...
Smoothing Chromosome chr5 ...
Smoothing Chromosome chr6 ...
Smoothing Chromosome chr7 ...
Smoothing Chromosome chr8 ...
Smoothing Chromosome chr9 ...
Smoothing Chromosome chrX ...
Smoothing Chromosome chrY ...
[1] "Done with detectDMR.slideWin\n"
No significant CpG-sites were identified based on current criteria!
-- output of sessionInfo():
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=C
[5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] grid parallel methods stats graphics grDevices utils
[8] datasets base
other attached packages:
[1] MASS_7.3-29
[2] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
[3] minfi_1.9.11
[4] bumphunter_1.2.0
[5] locfit_1.5-9.1
[6] iterators_1.0.6
[7] foreach_1.4.1
[8] Biostrings_2.30.1
[9] lattice_0.20-24
[10] methyAnalysis_1.4.2
[11] GenomicRanges_1.14.4
[12] XVector_0.2.0
[13] IRanges_1.20.6
[14] wateRmelon_1.2.2
[15] ROC_1.38.0
[16] IlluminaHumanMethylation450k.db_2.0.7
[17] org.Hs.eg.db_2.10.1
[18] RSQLite_0.11.4
[19] DBI_0.2-7
[20] AnnotationDbi_1.24.0
[21] limma_3.18.4
[22] methylumi_2.8.0
[23] matrixStats_0.8.14
[24] ggplot2_0.9.3.1
[25] reshape2_1.2.2
[26] scales_0.2.3
[27] lumi_2.14.1
[28] Biobase_2.22.0
[29] BiocGenerics_0.8.0
loaded via a namespace (and not attached):
[1] BSgenome_1.30.0 BiocInstaller_1.12.0 Formula_1.1-1
[4] GenomicFeatures_1.14.2 Gviz_1.6.0 Hmisc_3.14-0
[7] KernSmooth_2.23-10 Matrix_1.1-2 R.methodsS3_1.6.1
[10] RColorBrewer_1.0-5 RCurl_1.95-4.1 Rsamtools_1.14.2
[13] XML_3.98-1.1 affy_1.40.0 affyio_1.30.0
[16] annotate_1.40.0 beanplot_1.1 biomaRt_2.18.0
[19] biovizBase_1.10.7 bitops_1.0-6 cluster_1.14.4
[22] codetools_0.2-8 colorspace_1.2-4 dichromat_2.0-0
[25] digest_0.6.4 doRNG_1.5.5 genefilter_1.44.0
[28] genoset_1.14.0 gtable_0.1.2 illuminaio_0.2.0
[31] itertools_0.1-1 labeling_0.2 latticeExtra_0.6-26
[34] mclust_4.2 mgcv_1.7-28 multtest_2.18.0
[37] munsell_0.4.2 nleqslv_2.1 nlme_3.1-113
[40] nor1mix_1.1-4 pkgmaker_0.17.4 plyr_1.8
43] preprocessCore_1.24.0 proto_0.3-10 registry_0.2
[46] reshape_0.8.4 rngtools_1.2.3 rtracklayer_1.22.3
[49] siggenes_1.36.0 splines_3.0.2 stats4_3.0.2
[52] stringr_0.6.2 survival_2.37-7 tools_3.0.2
[55] xtable_1.7-1 zlibbioc_1.8.0
------------------------------------------------------------
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Subject: Job 5342893: <idat2dmrMA> Done
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