How to install MethylKit?
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s1432985 • 0
@s1432985-14503
Last seen 3.8 years ago

My problem is first of all, I am not a programmer but I need to use MethylKit for my job. So here is the thing: I cannot install it, let me paste it here, what R is saying:

Loading required package: GenomicRanges
Loading required package: stats4
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: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Error: package or namespace load failed for ‘methylKit’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘data.table’

I installed these as well, but in that case, Matrix and mcgv were not updated and I cannot update them neither.
So what shall I do? Can someone help me by telling me how to install these and make it work?
Thanks for advance!

methylkit Tutorial • 652 views
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@martin-morgan-1513
Last seen 9 weeks ago
United States

Install data.table, biocLite("data.table"). If that succeeds, try to install methylKit again. If it fails, either install the missing dependencies or report back here.

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Thank you for your answer, Sir.
I installed data.table and did as you told but it just doesn't work...

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but now you have to tell us how it 'just doesn't work'. If it is the same error 'there is no package called 'data.table'' then you have to show us how you installed data.table.

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