Chromosome information in MethyLumiM object
1
0
Entering edit mode
@francesco-mancuso-4483
Last seen 8.4 years ago
Hi group! I'm doing an analysis of methylation data from the Illumina Infinium 27K Methylation array using the /lumi/ package. I need to associate the CpGs with the respective chromosome. Does anyone know how to integrate the information about the chromosomes in a MethyLumiM object? Many thanks in advance, Francesco -- *Francesco Mattia Mancuso* - Bioinformatician at Bioinformatics Core Facility - Bioinformatician at Proteomics Core Facility CRG-Centre for Genomic Regulation C/ Dr. Aiguader, 88 Edif. PRBB 08003 Barcelona, Spain Telephone: +34 933160202 francesco.mancuso@crg.es <mailto:francesco.mancuso@crg.es> www.crg.es <http: pasteur.crg.es="" portal="" page="" portal="" internet=""/> [[alternative HTML version deleted]]
Proteomics Proteomics • 581 views
ADD COMMENT
0
Entering edit mode
Tim Triche ★ 4.2k
@tim-triche-3561
Last seen 2.4 years ago
United States
## AML is a MethyLumiM object; ## fData(AML) is its featureData > library(IlluminaHumanMethylation27k.db) > fData(AML)$chrom<- as.factor(unlist(mget(featureNames(AML), IlluminaHumanMethylation27kCHR))) > table(fData(AML)$chrom) 1 10 11 12 13 14 15 16 17 18 19 2287 848 1315 1268 399 684 643 900 1275 313 1449 2 20 21 22 3 4 5 6 7 8 9 1384 662 235 494 1255 830 955 1239 939 772 829 X Y 2 4 There are some NAs in the IlluminaHumanMethylation27k.db release currently available; I'll see about fixing those in the very near future, although it should be noted that there are a number of duplicates, repetitive sequences, and similarly undesirable bits in the 27k probes. It's up to the user to weed out the probes they don't want in that respect. --t On Fri, Feb 11, 2011 at 4:18 AM, Francesco Mancuso <francesco.mancuso@crg.eu> wrote: > Hi group! > I'm doing an analysis of methylation data from the Illumina Infinium 27K > Methylation array using the /lumi/ package. > I need to associate the CpGs with the respective chromosome. > > Does anyone know how to integrate the information about the chromosomes > in a MethyLumiM object? > > Many thanks in advance, > Francesco > > > -- > > *Francesco Mattia Mancuso* > - Bioinformatician at Bioinformatics Core Facility > - Bioinformatician at Proteomics Core Facility > > CRG-Centre for Genomic Regulation > C/ Dr. Aiguader, 88 > Edif. PRBB > 08003 Barcelona, Spain > > Telephone: +34 933160202 > francesco.mancuso@crg.es <mailto:francesco.mancuso@crg.es> > www.crg.es <http: pasteur.crg.es="" portal="" page="" portal="" internet=""/> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]
ADD COMMENT

Login before adding your answer.

Traffic: 516 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6