eshinesimida / subpathway-analysis Goto Github PK

Issue # 1:
mapkpathway<-try(parseKGML(paste(mdir,paths[6],sep="/")),TRUE)
There are only 4 pathways in SPIA package:
> paths [1] "hsa03013.xml" "hsa03050.xml" "hsa04914.xml" "hsa05210.xml"
So changed to paths[4].

Issue# 2:
KEGGpathway2Graph_c requires library(graph)

Issue #3
> gR<-KEGGsubpathway2subGraph(mapkpathway,diffgenes)
Error in KEGGsubpathway2subGraph(mapkpathway, diffgenes) : could not find function "expandKEGGsubPathway_gene"

Issue #4
> plotsubpathway(gR)
Error: could not find function "plotsubpathway"

> sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X Yosemite 10.10.5

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] grid stats4 parallel stats graphics grDevices utils [8] datasets methods base

other attached packages: [1] RColorBrewer_1.1-2 Rgraphviz_2.18.0 RBGL_1.50.0 [4] igraph_1.0.1 hgu133plus2.db_3.2.3 org.Hs.eg.db_3.4.0 [7] AnnotationDbi_1.36.0 IRanges_2.8.1 S4Vectors_0.12.0 [10] Biobase_2.34.0 graph_1.52.0 BiocGenerics_0.20.0 [13] XML_3.98-1.5 SPIA_2.26.0 KEGGgraph_1.32.0 [16] SubSPIA_0.1

loaded via a namespace (and not attached): [1] DBI_0.5-1 magrittr_1.5 RSQLite_1.0.0 tools_3.3.2