how to find a pathway using a set of metabolites

Question

[Learner]

I have a Metabolomics data with a p value, I want to know which ways I can find pathways, as an example please use the following data

df<- structure(list(rn = c("1-Methylhistidine", "L-Kynurenine", "N6,N6,N6-Trimethyl-L-lysine", 
"Putrescine", "Cytidine", "Xanthosine", "N-Alpha-acetyllysine", 
"L-Phenylalanine", "L-Arginine", "Pantothenic acid"), P.Value = c(3.68760885497216e-05, 
0.000294447368552433, 0.00186310350410466, 0.00211110071314893, 
0.00348498422603502, 0.00373568863130606, 0.0082476384775719, 
0.0177605396545179, 0.0224866727309657, 0.0337353837405139)), row.names = c(NA, 
-10L), class = c("data.table", "data.frame"), .internal.selfref = <pointer: 0x1020162e0>)

Answer 1

[Kevin Blighe]

Try MetaboAnalyst

Kevin

[Learner]

@Kevin Blighe I want to use it in R, I found their package but it seems not very straightforward. any idea?

Answer 2

[bbmisraccb]

Hi,

Try FELLA: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2487-5 and/ or Lilikoi: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6290884/ both on CRAN, and are new and active ones!

Thanks,