fadhlyemen/lilikoi_fadhl

Lilikoi is a novel tool for personalized pathway analysis of metabolomics data.

Prerequisites

To install all the required packages without overwriting your installed packages, you can run the below lines:

list.of.packages <- c("ggplot2", "caret","dplyr ","pathifier","RWeka","infotheo","pROC","reshape2","corrplot","Hmisc")
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)

Installation

devtools::install_github("FADHLyemen/lilikoi_Fadhl")

if you have problem with installing Rweka as it requirtes Java, you can reconfiguring R from the command line by runing the below line:

R CMD javareconf

Built With

• Fadhl Alakwaa https://github.com/FADHLyemen
• Sijia Huang https://github.com/scarlettcanny

Example Code

https://github.com/FADHLyemen/lilikoi_Fadhl/blob/master/lilikoi_example.ipynb

lilikoi_fadhl's Issues

PDSfun function error

Hello,

Loaddata(file="./Data/DuplMetabolomics_clean.csv")
Metabolite_pathway_table=MetaTOpathway('name')
PDSmatrix= PDSfun(Metabolite_pathway_table)

Loading required package: pathifier
robust_score_bydist. min_exp= 0 , min_std= 0
Error in quantify_pathways_deregulation(as.matrix(newData), row.names(newData), :
invalid dimentions
Calls: PDSfun -> quantify_pathways_deregulation

If you can assist with the reason behind this error and how can I solve it?

Thanks,