Hello,
I am wanting to use ChAMP to analyse the data from 2 MethylationEPIC chips. I am very new to R/ChAMP, and am having some difficulties. Any help would be greatly appreciated!
I have installed the ChAMP programme from Bioconductor, and then performed the library(ChAMP) function. However, it seems that some of the packages aren't loading properly. I am also not able to load my data into ChAMP. (please see code below). I've tried loading the packages in ChAMP separately, and this doesn't seem to be making a difference. I have checked that my csv files are correctly formatted, and my chip files are idat files. I've triple checked that I have the latest version of R, and have performed all necessary updates. I have also uninstalled and reinstalled everything, and tried this on 2 different computers, with no luck.
Has anyone else experienced this, or has any idea what I can do to solve this problem, as I seem to be going round in circles, which is incredibly frustrating!
Thank you in advance for your suggestions!
Best wishes
Charlie
> library(ChAMP)
Loading required package: minfi
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap,
parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, cbind, colMeans, colnames, colSums, do.call,
duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position,
rank, rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'. To cite
Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: ‘matrixStats’
The following objects are masked from ‘package:Biobase’:
anyMissing, rowMedians
Attaching package: ‘DelayedArray’
The following objects are masked from ‘package:matrixStats’:
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from ‘package:base’:
apply
Loading required package: Biostrings
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:DelayedArray’:
type
The following object is masked from ‘package:base’:
strsplit
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Error: package or namespace load failed for ‘bumphunter’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘digest’
Error: package ‘bumphunter’ could not be loaded
> testDir=system.file("extdata", package="ChAMPdata")
> myLoad<-champ.load(testDir,arraytype="EPIC")
Error in champ.load(testDir, arraytype = "EPIC") :
could not find function "champ.load"
> myImpute<-champ.impute
Error: object 'champ.impute' not found
