RnBeads error: option

Stephen Hwang

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Apr 6, 2016, 2:35:49 PM4/6/16

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I’m using the source code from here to test out the example RRBS dataset. When I try to set the first set of options (bolded below), I get the following error (also see attached):

Error in rnb.options(identifiers.column = "sampleID", import.bed.style = "BisSNP", :

invalid value for option assembly

Is there something that I am missing?

################################################################################

# (1) Set analysis options

################################################################################

rnb.options(

identifiers.column = "sampleID",

import.bed.style = "BisSNP",

assembly = "mm9",

filtering.low.coverage.masking = TRUE,

filtering.greedycut = FALSE,

filtering.missing.value.quantile = 0.5,

filtering.high.coverage.outliers = TRUE

)

# optionally disable some parts of the analysis to reduce runtime

rnb.options(

exploratory.intersample = FALSE,

exploratory.region.profiles = character(0),

differential.comparison.columns = c("differentiation_level",

"blood_lineage", "cmp_blood_CLP_CMP"),

differential.report.sites = FALSE

)

################################################################################

# (2) Run the analysis

################################################################################

rnb.run.analysis(

dir.reports=reportDir,

sample.sheet=sampleSheet,

data.dir=bedDir,

data.type="bs.bed.dir"

)

rnbeads_compatibility2.JPG

Stephen Hwang

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Apr 6, 2016, 7:32:19 PM4/6/16

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Here's my session info

> sessionInfo()

R version 3.2.4 Revised (2016-03-16 r70336)

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

[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C

[5] LC_TIME=English_United States.1252

attached base packages:

[1] grid stats4 parallel stats graphics grDevices utils datasets

[9] methods base

other attached packages:

[1] RnBeads_1.2.2 plyr_1.8.3

[3] methylumi_2.16.0 minfi_1.16.1

[5] bumphunter_1.10.0 locfit_1.5-9.1

[7] iterators_1.0.8 foreach_1.4.3

[9] Biostrings_2.38.4 XVector_0.10.0

[11] lattice_0.20-33 FDb.InfiniumMethylation.hg19_2.2.0

[13] org.Hs.eg.db_3.2.3 RSQLite_1.0.0

[15] DBI_0.3.1 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2

[17] GenomicFeatures_1.22.13 AnnotationDbi_1.32.3

[19] reshape2_1.4.1 scales_0.4.0

[21] illuminaio_0.12.0 matrixStats_0.50.1

[23] limma_3.26.9 gridExtra_2.2.1

[25] gplots_3.0.1 ggplot2_2.1.0

[27] fields_8.3-6 maps_3.1.0

[29] spam_1.3-0 ff_2.2-13

[31] bit_1.1-12 cluster_2.0.3

[33] RColorBrewer_1.1-2 MASS_7.3-45

[35] bsseq_1.6.0 Rcpp_0.12.4

[37] BiocInstaller_1.20.1 SummarizedExperiment_1.0.2

[39] Biobase_2.30.0 GenomicRanges_1.22.4

[41] GenomeInfoDb_1.6.3 IRanges_2.4.8

[43] S4Vectors_0.8.11 BiocGenerics_0.16.1

loaded via a namespace (and not attached):

[1] nlme_3.1-126 bitops_1.0-6 tools_3.2.1

[4] doRNG_1.6 nor1mix_1.2-1 KernSmooth_2.23-15

[7] colorspace_1.2-6 base64_1.1 preprocessCore_1.32.0

[10] chron_2.3-47 pkgmaker_0.22 rtracklayer_1.30.4

[13] caTools_1.17.1 quadprog_1.5-5 genefilter_1.52.1

[16] stringr_1.0.0 digest_0.6.9 Rsamtools_1.22.0

[19] siggenes_1.44.0 R.utils_2.2.0 GEOquery_2.36.0

[22] mclust_5.2 BiocParallel_1.4.3 gtools_3.5.0

[25] R.oo_1.20.0 RCurl_1.95-4.8 magrittr_1.5

[28] futile.logger_1.4.1 munsell_0.4.3 R.methodsS3_1.7.1

[31] stringi_1.0-1 zlibbioc_1.16.0 gdata_2.17.0

[34] splines_3.2.1 multtest_2.26.0 annotate_1.48.0

[37] beanplot_1.2 igraph_1.0.1 corpcor_1.6.8

[40] rngtools_1.2.4 mixOmics_5.2.0 codetools_0.2-14

[43] biomaRt_2.26.1 futile.options_1.0.0 XML_3.98-1.4

[46] lambda.r_1.1.7 data.table_1.9.6 gtable_0.2.0

[49] reshape_0.8.5 xtable_1.8-2 survival_2.38-3

[52] ellipse_0.3-8 GenomicAlignments_1.6.3 registry_0.3

[55] rgl_0.95.1441

Fabian

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Apr 7, 2016, 4:11:51 AM4/7/16

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Hi Stephen,
looks like the RnBeads.mm9 package was not installed on your system. Could you install it from bioconductor (http://bioconductor.org/packages/release/data/experiment/html/RnBeads.mm9.html) and try again?

Best,
Fabian
__________________________________________________
    The RnBeads Developers
    Max Planck Institute for Informatics
    Computational Biology and Applied Algorithmics Department

    Campus E 1.4
    Room 509
    66123 Saarbrücken
    Germany

    Phone: +49 (681) 9325 3009
    Email: rnb...@mpi-inf.mpg.de
    http://rnbeads.mpi-inf.mpg.de

Stephen Hwang

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Apr 7, 2016, 9:12:31 AM4/7/16

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Hi Fabian,

Thanks for taking a look. I tried to install the mm9 (for the test dataset) and mm10 (which we ultimately need) assembly but the installation fails (see attached). Is this due to differences in R version?

mm9 fail.JPG

Fabian

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Apr 8, 2016, 4:24:23 AM4/8/16

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Not entirely sure, but that could be.

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