egeulgen
commented
4 years ago hey @ASPalacio,
The issue was when you save the PIN file, you save it with quotes=TRUE (default behavior) so the active subnetwork search module failed to find any genes in the PIN. The PIN should be saved as:
write.table(pmg_string_pin,
file = path2SIF,
col.names = FALSE,
row.names = FALSE,
sep = "\t",
quote = FALSE)When I did so, I got 32 enriched pathways for your data. (this number may differ) I will fix that mistake in the vignette as well, thanks for opening the issue!
ASPalacio
Hello,
I'm new with pathfindR and I'm trying to do enrichment analysis on non human samples. I have followed the m.musculus example. I dowloaded the PIN from STRING, and the codes in the PIN are the same that in the kegg_genes and kegg_description lists. But pathfindR is not able to find the genes in the input in the PIN and I don't know what's going wrong
To Reproduce I attached the script, RDS objects with kegg_genes, kegg_description and the input data, and the PIN.
Screenshots Output of R console:
issue.zip
Desktop (please complete the following information):
R Session Information: R version 4.0.0 (2020-04-24) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.4
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] biomaRt_2.44.0 pathview_1.28.0 org.Hs.eg.db_3.11.1 AnnotationDbi_1.50.0
[5] KEGGREST_1.28.0 DESeq2_1.28.1 SummarizedExperiment_1.18.1 DelayedArray_0.14.0
[9] matrixStats_0.56.0 Biobase_2.48.0 GenomicRanges_1.40.0 GenomeInfoDb_1.24.0
[13] IRanges_2.22.1 S4Vectors_0.26.1 BiocGenerics_0.34.0 dplyr_0.8.5
[17] pathfindR_1.5.0.9009
loaded via a namespace (and not attached): [1] colorspace_1.4-1 ellipsis_0.3.1 rprojroot_1.3-2 XVector_0.28.0 fs_1.4.1
[6] rstudioapi_0.11 farver_2.0.3 remotes_2.1.1 graphlayouts_0.7.0 ggrepel_0.8.2
[11] bit64_0.9-7 fansi_0.4.1 codetools_0.2-16 splines_4.0.0 doParallel_1.0.15
[16] geneplotter_1.66.0 knitr_1.28 polyclip_1.10-0 pkgload_1.0.2 annotate_1.66.0
[21] dbplyr_1.4.3 png_0.1-7 graph_1.66.0 ggforce_0.3.1 BiocManager_1.30.10
[26] compiler_4.0.0 httr_1.4.1 backports_1.1.7 assertthat_0.2.1 Matrix_1.2-18
[31] cli_2.0.2 tweenr_1.0.1 htmltools_0.4.0 prettyunits_1.1.1 tools_4.0.0
[36] igraph_1.2.5 gtable_0.3.0 glue_1.4.1 GenomeInfoDbData_1.2.3 rappdirs_0.3.1
[41] Rcpp_1.0.4.6 vctrs_0.3.0 Biostrings_2.56.0 iterators_1.0.12 ggraph_2.0.2
[46] xfun_0.13 stringr_1.4.0 ps_1.3.3 testthat_2.3.2 lifecycle_0.2.0
[51] devtools_2.3.0 XML_3.99-0.3 zlibbioc_1.34.0 MASS_7.3-51.6 scales_1.1.1
[56] tidygraph_1.2.0 hms_0.5.3 KEGGgraph_1.48.0 RColorBrewer_1.1-2 yaml_2.2.1
[61] curl_4.3 memoise_1.1.0 gridExtra_2.3 ggplot2_3.3.0 stringi_1.4.6
[66] RSQLite_2.2.0 highr_0.8 genefilter_1.70.0 desc_1.2.0 foreach_1.5.0
[71] pkgbuild_1.0.8 BiocParallel_1.22.0 rlang_0.4.6 pkgconfig_2.0.3 bitops_1.0-6
[76] evaluate_0.14 lattice_0.20-41 purrr_0.3.4 labeling_0.3 bit_1.1-15.2
[81] tidyselect_1.1.0 processx_3.4.2 magrittr_1.5 R6_2.4.1 magick_2.3
[86] DBI_1.1.0 pillar_1.4.4 withr_2.2.0 survival_3.1-12 RCurl_1.98-1.2
[91] tibble_3.0.1 crayon_1.3.4 BiocFileCache_1.12.0 rmarkdown_2.1 usethis_1.6.1
[96] viridis_0.5.1 progress_1.2.2 locfit_1.5-9.4 grid_4.0.0 blob_1.2.1
[101] callr_3.4.3 Rgraphviz_2.32.0 digest_0.6.25 xtable_1.8-4 tidyr_1.0.3
[106] openssl_1.4.1 munsell_0.5.0 viridisLite_0.3.0 sessioninfo_1.1.1 askpass_1.1
Additional context java --version java 14.0.1 2020-04-14 Java(TM) SE Runtime Environment (build 14.0.1+7) Java HotSpot(TM) 64-Bit Server VM (build 14.0.1+7, mixed mode, sharing)