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I cannot figure out why I am unable to subset features of my methy Lumi Set.However, a potential issue might be with the annotation.Installing package(s) ‘Illumina Human Methylation450k’ Old packages: 'stringi', 'Variant Annotation' Update all/some/none?
Because they removed the sex chromosomes, there is no point in me keeping them. Any idea why the feature Filter function will not work for me?
Warning message: In .feature Filter(eset, require.entrez = require.entrez, require. GOBP, : Human Methylation450k probes annotate to multiple accessions(!
There are an awful lot of sites on chr X that matter 2) why not add a term for gender in the regression fit / DMRcate / whatever instead?
3) why not check that the sex of samples (from X copy number and/or X inactivation) matches the putative sex of the subjects? methylum IDAT, to be sure, and I'll patch that as soon as I have a moment (to point to the somewhat extensive vignette, and perhaps add a few functions for the above, which have been languishing in another package).
IDAT files using the "methy Lumi" package and I am planning on pre-processing the data using some of the normalization functions in the "wate Rmelon" package: # Read sample data.
# pheno Data is a data.frame with the row names = Sentrix Position_barcode # and columns containing sample group, age and gender.
YO, pdat = pheno Data, idat Path = "/Users/Martens/Desktop/08272014/IDATs") 2 Subset of 485577 features.1) that's a Golden Gate example, there are no chr Y probes on that platform 2) here is a vignette-length 450k example for methylum IDAT (which I should point to, now that you mention it, in the man page for methylum IDAT): R keep Seqlevels(map To Genome(mset450k), 'chr Y') class: Genomic Methyl Set dim: 416 10 metadata(0): assays(2): Meth Unmeth rownames(416): cg13654344 cg04169747 ...
cg08265308 cg14273923 row Ranges metadata column names(0): colnames(10): TCGA1 TCGA2 ...
barcodes (10 total) var Metadata: label Description feature Data feature Names: cg00000029 cg00000108 ...Tags: Adult Dating, affair dating, sex dating