Dear Bioconductors,
I've been trying to set up data to run a DMR analysis for the Illumina Infinium HumanMethylation450. I have a matrix of probes and individual human id's, but I need to merge these with probe specific data, especially location data for the DMR analysis (seqLM, but still learning so open to suggestions).
I've found myself entirely unable to install any annotation file for the probes, and I've tried several.
illuminahumanmethylation450k.db ======= * Outdated, I gather.
library FDb.InfiniumMethylation.hg19 OR IlluminaHumanMethylation450kanno.ilmn12.hg19 ==== ERROR
------------------
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Error in unloadNamespace(package) :
namespace ‘GenomeInfoDb’ is imported by ‘GenomicRanges’ so cannot be unloaded
Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, :
Package ‘GenomeInfoDb’ version 1.8.1 cannot be unloaded
------------------
I've tried:
remove.packages('GenomeInfoDb')
biocLite('GenomeInfoDb')
with the former providing the output:
--
Removing package from ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
(as ‘lib’ is unspecified)
--
I'm sort of at a loss. I am decent with Stats and R (but NOT a programmer), but am just figuring out how to work with and manipulate the complex datasets that are GRanges, IRanges, etc. in these deep tree lists.
I cannot for the life of me figure out why there are so many Illumina annotation files, and why none of them will load properly. Once I have that, then I can finally figure out how to subset and merge and create a dataset usable for the DMR analysis.
Q. How should I go about solving the above problem loading a Illumina 450K annotation data, with genomic location, gene names, and all that jazz, and then merge by probe name to my other dataset?
Many many thanks,
CPR
==============
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] Biobase_2.32.0 IRanges_2.6.1 S4Vectors_0.10.2 BiocGenerics_0.18.0 BiocInstaller_1.22.3
[6] repmis_0.5 ff_2.2-13 bit_1.1-12 dplyr_0.5.0 HardyWeinberg_1.5.6
[11] mice_2.25 Rcpp_0.12.6 stargazer_5.2 colorRamps_2.3 scales_0.4.0
[16] lmtest_0.9-34 zoo_1.7-13 sjmisc_1.8 QuantPsyc_1.5 boot_1.3-18
[21] nlme_3.1-128 MASS_7.3-45 lsr_0.5 lmSupport_2.9.4 Hmisc_3.17-4
[26] ggplot2_2.1.0 Formula_1.2-1 survival_2.39-5 lattice_0.20-33 car_2.1-2
[31] reshape2_1.4.1 plyr_1.8.4 doBy_4.5-15 readstata13_0.8.2 gdata_2.17.0
[36] foreign_0.8-66 seqlm_0.1
loaded via a namespace (and not attached):
[1] pbkrtest_0.4-6 httr_1.2.1 RColorBrewer_1.1-2 GenomeInfoDb_1.8.3 R.cache_0.12.0
[6] tools_3.3.1 R6_2.1.2 rpart_4.1-10 DBI_0.4-1 lazyeval_0.2.0
[11] mgcv_1.8-13 colorspace_1.2-6 nnet_7.3-12 raster_2.5-8 sp_1.2-3
[16] gridExtra_2.2.1 mnormt_1.5-4 chron_2.3-47 quantreg_5.26 SparseM_1.7
[21] sandwich_2.3-4 unmarked_0.11-0 mvtnorm_1.0-5 psych_1.6.6 AICcmodavg_2.0-4
[26] stringr_1.0.0 digest_0.6.9 minqa_1.2.4 R.utils_2.3.0 stringdist_0.9.4.1
[31] XVector_0.12.0 lme4_1.1-12 VGAM_1.0-2 gtools_3.5.0 acepack_1.3-3.3
[36] R.oo_1.20.0 magrittr_1.5 modeltools_0.2-21 Matrix_1.2-6 munsell_0.4.3
[41] R.methodsS3_1.7.1 stringi_1.1.1 multcomp_1.4-6 gvlma_1.0.0.2 zlibbioc_1.18.0
[46] grid_3.3.1 haven_0.2.1 splines_3.3.1 GenomicRanges_1.24.2 codetools_0.2-14
[51] latticeExtra_0.6-28 data.table_1.9.6 nloptr_1.0.4 foreach_1.4.3 MatrixModels_0.4-1
[56] gtable_0.2.0 tidyr_0.5.1 reshape_0.8.5 assertthat_0.1 coin_1.1-2
[61] xtable_1.8-2 tibble_1.1 iterators_1.0.8 cluster_2.0.4 TH.data_1.0-7
