how to find a pathway using a set of metabolites
2
1
Entering edit mode
2.7 years ago
Learner ▴ 250

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>)
R • 576 views
ADD COMMENT
1
Entering edit mode
2.7 years ago

Try MetaboAnalyst

Kevin

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
2.7 years ago
bbmisraccb ▴ 70

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,

ADD COMMENT

Login before adding your answer.

Traffic: 1270 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6