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Question: chipenrich mm10 error
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gravatar for jamie.gearing
20 months ago by
jamie.gearing40 wrote:

I have encountered an error while trying to use the chipenrich package with the mm10 genome. Here is a small example:

library(chipenrich)
peaks <- data(peaks_E2F4, package = 'chipenrich.data')
results <- chipenrich(head(peaks), out_name=NULL, genome = "mm10", genesets = c("GOBP", "GOCC", "GOMF"))

# Error in chipenrich(head(peaks), out_name = NULL, genome = "mm10") : 
#   Invalid organism / geneset(s) combination requested: mmu TRUE
# In addition: Warning message:
#   In if (file.exists(genesets)) { :
#       the condition has length > 1 and only the first element will be used​

I think the problem might lie on line 33 of the chipenrich() function. For "mmu" and these gene sets:

any(supported_genesets()$organism == "mmu" & c("GOBP", "GOCC", "GOMF") == supported_genesets()$geneset)
# [1] FALSE

Perhaps this should be:

any(supported_genesets()$organism == "mmu" & supported_genesets()$geneset %in% c("GOBP", "GOCC", "GOMF"))
# [1] TRUE

Thanks.

 

sessionInfo()

# R version 3.3.2 (2016-10-31)
# Platform: x86_64-apple-darwin13.4.0 (64-bit)
# Running under: macOS Sierra 10.12.3
# 
# locale:
#   [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
# 
# attached base packages:
#   [1] stats     graphics  grDevices utils     datasets  methods   base     
# 
# other attached packages:
#   [1] chipenrich_1.12.0
# 
# loaded via a namespace (and not attached):
#   [1] httr_1.2.1             tidyr_0.6.1            jsonlite_1.3           viridisLite_0.1.3      splines_3.3.2          Formula_1.2-1         
# [7] shiny_1.0.0            assertthat_0.1         stats4_3.3.2           latticeExtra_0.6-28    backports_1.0.5        lattice_0.20-34       
# [13] quantreg_5.29          limma_3.30.12          digest_0.6.12          GenomicRanges_1.26.3   RColorBrewer_1.1-2     XVector_0.14.0        
# [19] checkmate_1.8.2        colorspace_1.3-2       sandwich_2.3-4         rms_5.1-0              htmltools_0.3.5        httpuv_1.3.3          
# [25] Matrix_1.2-8           plyr_1.8.4             SparseM_1.74           chipenrich.data_1.10.0 zlibbioc_1.20.0        purrr_0.2.2           
# [31] xtable_1.8-2           mvtnorm_1.0-6          scales_0.4.1           MatrixModels_0.4-1     htmlTable_1.9          tibble_1.2            
# [37] mgcv_1.8-17            IRanges_2.8.1          ggplot2_2.2.1          TH.data_1.0-8          nnet_7.3-12            BiocGenerics_0.20.0   
# [43] lazyeval_0.2.0         survival_2.40-1        magrittr_1.5           mime_0.5               polspline_1.1.12       MASS_7.3-45           
# [49] nlme_3.1-131           foreign_0.8-67         colourpicker_0.3       tools_3.3.2            data.table_1.10.4      multcomp_1.4-6        
# [55] stringr_1.2.0          plotly_4.5.6.9000      S4Vectors_0.12.1       munsell_0.4.3          cluster_2.0.5          GenomeInfoDb_1.10.3   
# [61] grid_3.3.2             RCurl_1.95-4.8         htmlwidgets_0.8        miniUI_0.1.1           bitops_1.0-6           base64enc_0.1-3       
# [67] codetools_0.2-15       gtable_0.2.0           DBI_0.5-1              R6_2.2.0               gridExtra_2.2.1        zoo_1.7-14            
# [73] knitr_1.15.1           dplyr_0.5.0            Hmisc_4.0-2            stringi_1.1.2          parallel_3.3.2         Rcpp_0.12.9           
# [79] rpart_4.1-10           acepack_1.4.1         

 

ADD COMMENTlink modified 20 months ago by rcavalca120 • written 20 months ago by jamie.gearing40
1
gravatar for rcavalca
20 months ago by
rcavalca120
United States
rcavalca120 wrote:

Yikes! Thank you for pointing this out!

I just pushed a patch (v1.12.1) to the release branch of Bioconductor. You can wait for it to work through the build system, or you can install the version with devtools::install_github('Bioconductor-mirror/chipenrich@release-3.4').

Thanks for using chipenrich.

ADD COMMENTlink written 20 months ago by rcavalca120

Thanks very much for such a fast response! This package is just what I need, so I am very grateful.

ADD REPLYlink written 20 months ago by jamie.gearing40
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