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Hello Peters,
I have used package called DMRcate to analyse 450k data. I want to find the gene which associates the DMRs.And I met some questions.The outputs include gene_assoc, group, hg19coord, no.probes, minpval, meanpval and maxbetafc,when I used the old version to analyse 450k data.
But when I update the package,the outputs became coord, no.cpgs, minfdr, Stouffer, maxbetafc,meanbetafc.There is no result of "gene_assoc".I want to find the gene names associating "coord",can you help me ? Can you please tel me how to associate the gene by using the newest DMRcate packages.
There follow the output results of the newest DMRcate.
coord no.cpgs minfdr Stouffer maxbetafc meanbetafc
63999 chr6:33156164-33181870 265 0 0 -0.5008031 -0.02648790
63997 chr6:33128825-33149777 150 0 0 0.4176126 0.08611966
63917 chr6:32144195-32161004 128 0 0 -0.2574513 -0.03184096
63914 chr6:32114490-32123701 124 0 0 -0.4377015 -0.06195576
63889 chr6:31935801-31940855 101 0 0 -0.1555205 -0.02401999
12564 chr11:31817810-31841980 100 0 0 -0.4611059 -0.17113506
There follow the output results of the older DMRcate.
gene_assoc group hg19coord no.probes minpval meanpval maxbetafc LOC100132215,OTX1 Body,TSS200,TSS1500 chr2:63273684-63287288 88 0 1.53809e-08 -0.1045803
Thank you !
The
extractRanges()function now appends promoter associations from Gencode/Ensembl instead. I find this annotation more reliable than Illumina's. Have a look at page 4 of the vignette:https://bioconductor.org/packages/release/bioc/vignettes/DMRcate/inst/doc/DMRcate.pdf
Cheers,
Tim
Tim,
Thanks for your reply.And now I meet a new question.I can not load the DMRcate package.
There follows the error.
Loading required package: splines
Loading required package: DMRcatedata
Error: package or namespace load failed for 'DMRcate' in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/data/users/robots/software/R_Bioconductor/R_Bioconductor-3.4.2/lib64/R/library/VariantAnnotation/libs/VariantAnnotation.so':
/lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by /data/users/robots/software/R_Bioconductor/R_Bioconductor-3.4.2/lib64/R/library/VariantAnnotation/libs/VariantAnnotation.so)
Can you give me some advise?
Thank you!
This is a problem with your version of zlib, not DMRcate. Looks like you need to update the version of zlib on your machine. This thread may be of help: https://www.biostars.org/p/89217/
Cheers,
Tim