Question

liftover probe annotation from hg19 to hg38 for methylation array data using minfi (EPIC methylation array data)

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Entering edit mode

brendan.miller • 0

@brendanmiller-20310

Last seen 5.1 years ago

Hello, I am trying to construct an annotation file and convert hg19 coordinates to hg38. The start of my code is as follows:

library(minfi)    
library(rtracklayer)
library(GenomicRanges)
allAnn=getAnnotation(hgscNorm)

However, I receive the following error:

> allAnn=getAnnotation(hgscNorm)
Error in is(object, "MethylSet") : object 'hgscNorm' not found

I have tried installing hgscNorm with:

> BiocManager::install("hgscNorm")

but I get the following output:

Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.3 (2019-03-11)
Installing package(s) 'hgscNorm'
installation path not writeable, unable to update packages: Matrix, mgcv
Warning message:
package ‘hgscNorm’ is not available (for R version 3.5.3)

I have also tried:

> BiocInstaller::biocLite(c("hgscNorm"))

but get the following output:

BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.32.1), R version 3.5.3.
Temporarily using Bioconductor version 2.13
Installing package(s) 'hgscNorm'
Warning: unable to access index for repository http://bioconductor.org/packages/2.13/bioc/bin/macosx/el-capitan/contrib/3.5:
  cannot open URL 'http://bioconductor.org/packages/2.13/bioc/bin/macosx/el-capitan/contrib/3.5/PACKAGES'
Warning: unable to access index for repository http://bioconductor.org/packages/2.13/data/annotation/bin/macosx/el-capitan/contrib/3.5:
  cannot open URL 'http://bioconductor.org/packages/2.13/data/annotation/bin/macosx/el-capitan/contrib/3.5/PACKAGES'
Warning: unable to access index for repository http://bioconductor.org/packages/2.13/data/experiment/bin/macosx/el-capitan/contrib/3.5:
  cannot open URL 'http://bioconductor.org/packages/2.13/data/experiment/bin/macosx/el-capitan/contrib/3.5/PACKAGES'
Warning: unable to access index for repository http://bioconductor.org/packages/2.13/extra/bin/macosx/el-capitan/contrib/3.5:
  cannot open URL 'http://bioconductor.org/packages/2.13/extra/bin/macosx/el-capitan/contrib/3.5/PACKAGES'
Warning messages:
1: package ‘hgscNorm’ is not available (for R version 3.5.3) 
2: installed directory not writable, cannot update packages 'Matrix', 'mgcv'

Do you know what the problem is and how I can install hgscNorm?

Thank you, Brendan

annotation probe software error EPIC methylation array • 2.1k views

ADD COMMENT • link 5.1 years ago brendan.miller • 0

score 0 · Answer 1 · 2019-03-27

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Entering edit mode

shepherl 3.8k

@lshep

Last seen just now

United States

Your are trying to pass into a function something that has not been defined yet. hgscNorm is not the name of a package. In should be the input to the function getAnnotation.

library(minfi)    
library(rtracklayer)
library(GenomicRanges)
allAnn=getAnnotation(hgscNorm)
Error in is(object, "MethylSet") : object 'hgscNorm' not found

hgscNorm has not been defined in the code you provide. It should be a minfi object. You will need to look at the minfi help pages to figure out how to create this object from the data files you have.

ADD COMMENT • link 5.1 years ago shepherl 3.8k

0

Entering edit mode

Thank you. You're absolutely right. To clarify for others who may view this:

My previous code was the following:

### install packages
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("BiocInstaller", version = "3.8")
BiocManager::install("GenomicFeatures")
BiocManager::install("rtracklayer")
BiocManager::install("minfi")
BiocManager::install("IlluminaHumanMethylationEPICmanifest", version = "3.8")
BiocManager::install("IlluminaHumanMethylationEPICanno.ilm10b4.hg19", version = "3.8")
library(minfi) # https://bioconductor.org/packages/release/bioc/vignettes/minfi/inst/doc/minfi.html
library(rtracklayer)
library(GenomicRanges)

Read in IDAT methylation array data to build minfi object:

targets=read.metharray.sheet("data") # "data" = top level directory that contains 'slides' and IDAT files within (see minfi vignette)
targets$Basename=file.path(".","data",targets$Slide,paste(targets$Slide,targets$Array,sep="_"))
RGset=read.metharray.exp(targ = targets) # read in IDAT data and make minfi object

### RGset is minfi object with probe beta values and annotation information

annotation(RGset)["array"]="IlluminaHumanMethylationEPIC"
annotation(RGset)["annotation"]="ilm10b2.hg19"
getManifest(RGset) # needs "IlluminaHumanMethylationEPICmanifest" package

prob=preprocessIllumina(RGset)
probF=preprocessFunnorm(RGset) # needs "IlluminaHumanMethylationEPICanno.ilm10b4.hg19" package
beta=getBeta(probF) # beta values

Now I can liftover the annotation from hg19 to hg38 (what I was originally trying to do):

allAnn=getAnnotation(RBset) #previously was: allAnn=getAnnotation(hgscNorm) but 'hgscNorm' should actually be RBset; I actually want the annotation of this object...
annRanges= makeGRangesFromDataFrame(allAnn[,1:4],
                              keep.extra.columns=T,
                              ignore.strand=FALSE,
                              seqinfo=NULL,
                              seqnames.field=c("seqnames", "seqname",
                                               "chromosome", "chrom",
                                               "chr", "chromosome_name",
                                               "seqid"),
                              start.field="pos",
                              end.field="pos",
                              strand.field="strand",
                              starts.in.df.are.0based=FALSE)

chain=import.chain("hg19ToHg38.Over.chain") # file downloaded from UCSC
hg38Locs=liftOver(annRanges,chain)
hg38LocsDF=data.frame(hg38Locs)
rownames(hg38LocsDF)=hg38LocsDF$group_name
pos38=start(unlist(hg38Locs))
allAnn=data.frame(allAnn,"pos.hg19"=allAnn$pos)
allAnn$pos=rep(NA,dim(allAnn)[1])
allAnn[hg38LocsDF$Name,"pos"]=hg38LocsDF[,"start"]

ADD REPLY • link 5.1 years ago brendan.miller • 0