Question: chipenrich mm10 error
0
gravatar for jamie.gearing
2.0 years 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         

 

chipenrich • 446 views
ADD COMMENTlink modified 2.0 years ago by rcavalca130 • written 2.0 years ago by jamie.gearing40
Answer: chipenrich mm10 error
1
gravatar for rcavalca
2.0 years ago by
rcavalca130
United States
rcavalca130 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 2.0 years ago by rcavalca130

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

ADD REPLYlink written 2.0 years ago by jamie.gearing40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 191 users visited in the last hour