Question: DMRcate package :How to find the gene associated with coordinate
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gravatar for 574233829
15 months ago by
5742338290
5742338290 wrote:

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 !

ADD COMMENTlink written 15 months ago by 5742338290

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

 

ADD REPLYlink written 15 months ago by Tim Peters80

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!

 

 

 

ADD REPLYlink written 15 months ago by 5742338290

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

 

 

 

ADD REPLYlink written 15 months ago by Tim Peters80
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