edroaldo
commented
6 years ago Hi, I am sorry for my delayed response. It has being a while that I do not use this function actually. If I remember correctly, you need to have an DAVID account and provide your login information in the function call. Let me double-check it and get back to you later.
Thanks!
2018-04-09 13:24 GMT-04:00 JianmeiZhong notifications@github.com:
Hi,edroaldo, Thanks sincerely your previous helpful solutions again.Here I ask for your help again but it's in the part of running davidclustering function. :) the error reported like this:
cellrouter=davidclustering(cellrouter,paths,"./","./",email=NULL,ids) Error in fea_david(names(x), annotations = c("GOTERM_BP_ALL", "KEGG_PATHWAY", : Query url too long.
ids is a data frame generated by myself with two colmuns 'external_gene_name' and 'ensembl_gene_id' which contain all 432 clustering genes in cellrouter@clusters$paths$clustering.
sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server release 6.4 (Santiago) Matrix products: default BLAS/LAPACK: /root/miniconda2/lib/R/lib/libRblas.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8 [9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8 [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8 attached base packages: [1] grid stats4 parallel stats graphics grDevices utils [8] datasets methods base other attached packages: [1] bitops_1.0-6 genefilter_1.60.0 gplots_3.0.1 [4] mclust_5.4 plyr_1.8.4 igraph_1.2.1 [7] tsne_0.1-3 plotrix_3.7 ReactomePA_1.22.0 [10] clusterProfiler_3.6.0 DOSE_3.4.0 pheatmap_1.0.8 [13] reshape2_1.4.3 reshape_0.8.7 RDAVIDWebService_1.16.0 [16] ggplot2_2.2.1 GOstats_2.44.0 Category_2.44.0 [19] Matrix_1.2-12 AnnotationDbi_1.40.0 IRanges_2.12.0 [22] S4Vectors_0.16.0 Biobase_2.38.0 graph_1.56.0 [25] BiocGenerics_0.24.0 rJava_0.9-9 FGNet_3.12.0 [28] RCurl_1.95-4.10 loaded via a namespace (and not attached): [1] httr_1.3.1 tidyr_0.8.0 bit64_0.9-7 [4] splines_3.4.3 R.utils_2.6.0 gtools_3.5.0 [7] DO.db_2.9 rvcheck_0.0.9 RBGL_1.54.0 [10] blob_1.1.1 pillar_1.2.1 RSQLite_2.0 [13] backports_1.1.2 lattice_0.20-35 glue_1.2.0 [16] digest_0.6.15 RColorBrewer_1.1-2 checkmate_1.8.5 [19] qvalue_2.10.0 colorspace_1.3-2 R.oo_1.21.0 [22] GSEABase_1.40.1 XML_3.98-1.9 pkgconfig_2.0.1 [25] reactome.db_1.62.0 purrr_0.2.4 xtable_1.8-2 [28] GO.db_3.5.0 scales_0.5.0 gdata_2.18.0 [31] BiocParallel_1.12.0 tibble_1.4.2 annotate_1.56.2 [34] lazyeval_0.2.1 survival_2.41-3 magrittr_1.5 [37] memoise_1.1.0 R.methodsS3_1.7.1 hwriter_1.3.2 [40] tools_3.4.3 data.table_1.10.4-3 stringr_1.3.0 [43] munsell_0.4.3 compiler_3.4.3 caTools_1.17.1 [46] rlang_0.2.0 rappdirs_0.3.1 AnnotationForge_1.20.0 [49] gtable_0.2.0 DBI_0.8 R6_2.2.2 [52] gridExtra_2.3 graphite_1.24.1 bit_1.1-12 [55] fastmatch_1.1-0 fgsea_1.4.1 KernSmooth_2.23-15 [58] Rgraphviz_2.22.0 GOSemSim_2.4.1 stringi_1.1.7 [61] Rcpp_0.12.16 png_0.1-7
was any parameter set wrong?.... Thanks for your any guidance in advance~
Best, Jianmei Zhong
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Hi,edroaldo, Thanks sincerely your previous helpful solutions again.Here I ask for your help again but it's in the part of running davidclustering function. :) the error reported like this:
ids is a data frame generated by myself with two colmuns 'external_gene_name' and 'ensembl_gene_id' which contain all 432 clustering genes in cellrouter@clusters$paths$clustering.
was any parameter set wrong?.... Thanks for your any guidance in advance~
Best, Jianmei Zhong