Dear All,
I am trying to analyze CNV from SNP6 data. I've run through crlmm and now trying vanillaICE. At the moment I am just following the exact same lines listed on the vanillaICE tutorial (http://www.bioconductor.org/packages/release/bioc/vignettes/VanillaICE/inst/doc/crlmmDownstream.pdf)
And I got stuck basically at the first 5 lines! It is not obvious to me what I should do about this error. Any suggestion is appreciated.
Thanks!!
Below is the code ( basically the same as from the tutorial) :
library(oligoClasses) library(VanillaICE) library(crlmm) library(SNPchip) library(IRanges) library(foreach) data(cnSetExample, package="crlmm") ##registerDoSEQ() library(snow) library(doSNOW) cl <- makeCluster(2, type="SOCK") registerDoSNOW(cl) ocSamples(2) se <- as(cnSetExample, "SnpArrayExperiment")
And the above line is where I got the error:
Error in { : task 1 failed - "could not find function "calculateRTheta""
session info:
R version 3.2.0 (2015-04-16) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] doSNOW_1.0.12 iterators_1.0.7 snow_0.3-13 foreach_1.4.2 SNPchip_2.14.0 crlmm_1.26.0 [7] preprocessCore_1.30.0 oligoClasses_1.30.0 VanillaICE_1.30.0 GenomicRanges_1.20.3 GenomeInfoDb_1.4.0 IRanges_2.2.1 [13] S4Vectors_0.6.0 BiocGenerics_0.14.0 loaded via a namespace (and not attached): [1] Rcpp_0.11.6 compiler_3.2.0 BiocInstaller_1.18.2 plyr_1.8.2 XVector_0.8.0 tools_3.2.0 zlibbioc_1.14.0 [8] base64_1.1 bit_1.1-12 RSQLite_1.0.0 lattice_0.20-31 ff_2.2-13 Matrix_1.2-0 DBI_0.3.1 [15] mvtnorm_1.0-2 stringr_1.0.0 Biostrings_2.36.1 grid_3.2.0 Biobase_2.28.0 data.table_1.9.4 ellipse_0.3-8 [22] VGAM_0.9-8 reshape2_1.4.1 magrittr_1.5 codetools_0.2-11 matrixStats_0.14.0 splines_3.2.0 stringi_0.4-1 [29] chron_2.3-45 RcppEigen_0.3.2.4.0 illuminaio_0.10.0 affyio_1.36.0
On closer examination, much of the code you have run is actually blocked out in the vignette you are running. If you look at the R script rather than the vignette, you will see that this is the code being run:
Which runs without complication.