sales-lab / graphite Goto Github PK

Hi,
I am using graphite for my thesis project, but I have some initial problems, that I can't solve.

Following the vignette, I run this code:

kegg <- pathways("hsapiens", "kegg")
p <- kegg[[2]]
head(nodes(p))

But I actually get:

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'head': '.SigArgs' is shorter than '.SigLength' says it should be

I'm pretty new with R and I really don't know how to solve this situation.
How can I manage with this error?
Thank you so much!

Here my SessionInfo:

R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
[1] gplots_3.1.1         org.Hs.eg.db_3.11.4  AnnotationDbi_1.50.3 IRanges_2.24.0      
[5] S4Vectors_0.28.0     Biobase_2.50.0       BiocGenerics_0.36.0  graphite_1.34.0     
[9] igraph_1.2.6        

loaded via a namespace (and not attached):
 [1] graph_1.68.0       Rcpp_1.0.5         magrittr_2.0.1     rappdirs_0.3.1    
 [5] bit_4.0.4          R6_2.5.0           rlang_0.4.10       blob_1.2.1        
 [9] httr_1.4.2         caTools_1.18.1     tools_4.0.2        checkmate_2.0.0   
[13] KernSmooth_2.23-17 DBI_1.1.0          gtools_3.8.2       bit64_4.0.5       
[17] digest_0.6.27      bitops_1.0-6       vctrs_0.3.4        memoise_1.1.0     
[21] RSQLite_2.2.1      compiler_4.0.2     backports_1.2.1    pkgconfig_2.0.3

Hi

I wanted to use some arguments used by org.hs.db package in your convertidentifiers function but could not find the source code.

Hi

Thanks for this great package. I really appreciate the idea of building pathway by propagating through metabolites. I am using your package to convert different databases into graphNEL objects by the following commands.

kegg_pathway <- graphite::pathways("hsapiens", "kegg")
kegg_graph <- lapply(kegg_pathway, graphite::pathwayGraph, which = "protein")

after this I wanted to extract the edgeTypes for different pathway and I used

edge_type <- lapply(kegg_graph, function(g) unlist(graph::edgeData(g, attr = "edgeType")))

and I get the following error

Error in .verifyAttrName(attr, names(self@defaults)) :
unknown attribute name: ‘edgeType’
Called from: .verifyAttrName(attr, names(self@defaults))

however when I use the same command over a single pathway it works.

head(graph::edgeData(kegg_graph[[10]], attr =  "edgeType"))

head(graph::edgeData(kegg_graph[[10]], attr = "edgeType"))
$ENTREZID:10449|ENTREZID:1962
[1] "Process(indirect)"

$ENTREZID:10449|ENTREZID:30
[1] "Process(indirect)"

$ENTREZID:10449|ENTREZID:3030
[1] "Process(indirect)"

$ENTREZID:10449|ENTREZID:3032
[1] "Process(indirect)"

$ENTREZID:10449|ENTREZID:3033
[1] "Process(indirect)"

$ENTREZID:10449|ENTREZID:33
[1] "Process(indirect)"

I'll be glad if you can help me to debug this. Is this error due to an absence of edgeType in any of the element of the kegg_graph list?

Nurun

Hello @gbrsales, I'm a Sweave2Rmd volunteer. @jwokaty and I are trying to replace Bioconductor Sweave vignettes with R Markdown. It has many advantages over Sweave vignettes, such as R Markdown converts to HTML, uses BiocStyle, and is easier to maintain.

Would you consider accepting a pull request for the R Markdown version of the graphite/vignettes/graphite.Rnw vignette from one of our volunteers?

We'll ask you to review and accept the pull request. You'll also need to bump the version number in your DESCRIPTION file so that the Bioconductor build machines will recognize that a new version is available.

Thank you for your time, I look forward to your response.