In [1]:
library()
In [2]:
library(RUVSeq)
Loading required package: Biobase
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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: EDASeq
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Warning message:
"multiple methods tables found for 'arbind'"Warning message:
"multiple methods tables found for 'acbind'"
Attaching package: 'SummarizedExperiment'
The following objects are masked from 'package:IRanges':
acbind, arbind
Warning message:
"replacing previous import 'IRanges::arbind' by 'SummarizedExperiment::arbind' when loading 'GenomicAlignments'"Warning message:
"replacing previous import 'IRanges::acbind' by 'SummarizedExperiment::acbind' when loading 'GenomicAlignments'"Warning message:
"multiple methods tables found for 'left'"Warning message:
"multiple methods tables found for 'right'"
Attaching package: 'ShortRead'
The following objects are masked from 'package:GenomicAlignments':
left, right
Loading required package: edgeR
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
In [16]:
RUVg()
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'RUVg' for signature '"missing", "missing", "missing"'
Traceback:
1. RUVg()
2. (function (classes, fdef, mtable)
. {
. methods <- .findInheritedMethods(classes, fdef, mtable)
. if (length(methods) == 1L)
. return(methods[[1L]])
. else if (length(methods) == 0L) {
. cnames <- paste0("\"", vapply(classes, as.character,
. ""), "\"", collapse = ", ")
. stop(gettextf("unable to find an inherited method for function %s for signature %s",
. sQuote(fdef@generic), sQuote(cnames)), domain = NA)
. }
. else stop("Internal error in finding inherited methods; didn't return a unique method",
. domain = NA)
. })(list(structure("missing", package = "methods"), structure("missing", package = "methods"),
. structure("missing", package = "methods")), structure(function (x,
. cIdx, k, drop = 0, center = TRUE, round = TRUE, epsilon = 1,
. tolerance = 1e-08, isLog = FALSE)
. {
. standardGeneric("RUVg")
. }, generic = structure("RUVg", package = "RUVSeq"), package = "RUVSeq", group = list(), valueClass = character(0), signature = c("x",
. "cIdx", "k", "drop", "center", "round", "epsilon", "tolerance",
. "isLog"), default = `\001NULL\001`, skeleton = (function (x,
. cIdx, k, drop = 0, center = TRUE, round = TRUE, epsilon = 1,
. tolerance = 1e-08, isLog = FALSE)
. stop("invalid call in method dispatch to 'RUVg' (no default method)",
. domain = NA))(x, cIdx, k, drop, center, round, epsilon, tolerance,
. isLog), class = structure("nonstandardGenericFunction", package = "methods")),
. <environment>)
3. stop(gettextf("unable to find an inherited method for function %s for signature %s",
. sQuote(fdef@generic), sQuote(cnames)), domain = NA)
In [15]:
RUVr()
In [ ]:
RUVs()
In [9]:
limmaUsersGuide()
'/opt/conda/envs/ruvseq/lib/R/library/limma/doc/usersguide.pdf'
In [1]:
% ls
Error in parse(text = x, srcfile = src): <text>:1:1: unexpected input
1: % ls
^
Traceback:
In [2]:
?system
In [5]:
system("conda list -n ruvseq", intern = TRUE)
- '# packages in environment at /opt/conda/envs/ruvseq:'
- '#'
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- 'bioconductor-annotationdbi 1.38.0 r3.3.1_0 bioconda'
- 'bioconductor-aroma.light 3.4.0 r3.3.1_0 bioconda'
- 'bioconductor-biobase 2.34.0 r3.3.1_0 bioconda'
- 'bioconductor-biocgenerics 0.20.0 r3.3.1_0 bioconda'
- 'bioconductor-biocparallel 1.6.6 r3.3.1_0 bioconda'
- 'bioconductor-biomart 2.28.0 r3.3.1_0 bioconda'
- 'bioconductor-biostrings 2.42.1 r3.3.1_0 bioconda'
- 'bioconductor-deseq 1.24.0 r3.3.1_0 bioconda'
- 'bioconductor-edaseq 2.8.0 r3.3.1_0 bioconda'
- 'bioconductor-edger 3.16.5 r3.3.1_0 bioconda'
- 'bioconductor-genefilter 1.56.0 r3.3.1_0 bioconda'
- 'bioconductor-geneplotter 1.50.0 r3.3.1_0 bioconda'
- 'bioconductor-genomeinfodb 1.10.3 r3.3.1_0 bioconda'
- 'bioconductor-genomicalignments 1.8.4 r3.3.1_0 bioconda'
- 'bioconductor-genomicfeatures 1.26.4 r3.3.1_0 bioconda'
- 'bioconductor-genomicranges 1.26.4 r3.3.1_0 bioconda'
- 'bioconductor-iranges 2.8.2 r3.3.1_0 bioconda'
- 'bioconductor-limma 3.30.13 r3.3.1_0 bioconda'
- 'bioconductor-rsamtools 1.24.0 r3.3.1_0 bioconda'
- 'bioconductor-rtracklayer 1.34.2 r3.3.1_1 bioconda'
- 'bioconductor-ruvseq 1.8.0 r3.3.1_0 pjones'
- 'bioconductor-s4vectors 0.12.2 r3.3.1_0 bioconda'
- 'bioconductor-shortread 1.32.0 r3.3.1_0 bioconda'
- 'bioconductor-summarizedexperiment 1.2.3 r3.3.1_0 bioconda'
- 'bioconductor-xvector 0.14.1 r3.3.1_0 bioconda'
- 'bioconductor-zlibbioc 1.20.0 r3.3.1_0 bioconda'
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- 'freetype 2.5.5 2 '
- 'glib 2.50.2 1 '
- 'gsl 2.2.1 0 '
- 'harfbuzz 0.9.39 2 '
- 'icu 54.1 0 '
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- 'jpeg 9b 0 '
- 'krb5 1.13.2 0 '
- 'libffi 3.2.1 1 '
- 'libgcc 5.2.0 0 '
- 'libiconv 1.14 0 '
- 'libpng 1.6.30 1 '
- 'libsodium 1.0.10 0 '
- 'libssh2 1.8.0 0 '
- 'libtiff 4.0.6 3 '
- 'libxml2 2.9.4 0 '
- 'ncurses 5.9 10 '
- 'openssl 1.0.2l 0 '
- 'pango 1.40.3 1 '
- 'pcre 8.39 1 '
- 'pip 9.0.1 py27_1 '
- 'pixman 0.34.0 0 '
- 'python 2.7.13 0 '
- 'r 3.3.1 r3.3.1_1 r'
- 'r-argparse 1.0.1 py27r3.3.1_0 bioconda'
- 'r-base 3.3.1 6 r'
- 'r-base64enc 0.1_3 r3.3.1_0 r'
- 'r-bh 1.60.0_2 r3.3.1_0 bioconda'
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- 'r-codetools 0.2_15 r3.3.1_0 r'
- 'r-crayon 1.3.1 r3.3.1_0 r'
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- 'r-dbi 0.5_1 r3.3.1_0 r'
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- 'r-stringr 1.1.0 r3.3.1_0 bioconda'
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- 'r-withr 1.0.2 r3.3.1_0 r'
- 'r-xml 3.98_1.5 r3.3.1_0 r'
- 'r-xtable 1.8_2 r3.3.1_0 r'
- 'readline 6.2 2 '
- 'setuptools 27.2.0 py27_0 '
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- 'wheel 0.29.0 py27_0 '
- 'xz 5.2.3 0 '
- 'zeromq 4.1.5 0 '
- 'zlib 1.2.11 0 '
In [ ]:
Content source: alaindomissy/scbatch
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