Dear All,
I have the data of metabolic pathways in case and control, well there are pathways which are represented several times due to the involvement of reactions in case, well now I would like to see if the no. of reactions in metabolic pathways in the case are significant when compared to no. of reactions in the control sample. I have attached an excel sheet to this message which includes pathway names and the no. of reactions in case and control. My next step is to perform fisher exact test using R and to identify false discovery rate in R. kindly let me know how this could be performed by using R programme
Hello Yogita Kattimani
Try this one:
FDR(pvals, qlevel = 0.05)
Arguments
pvals
a vector of pvals on which to conduct the multiple testing
qlevel
the proportion of false positives desired
Good luck-
Hi,
Maybe the epiR package can help you. Here for more information https://cran.r-project.org/web/packages/epiR/epiR.pdf
For Pathway 1 this code works
# Load library
library(epiR)
# Case - control - reactions matrix
dat
Hello Yogita Kattimani
Try this one:
FDR(pvals, qlevel = 0.05)
Arguments
pvals
a vector of pvals on which to conduct the multiple testing
qlevel
the proportion of false positives desired
Good luck-
You can use:
fisher.test(case, control)
## case=case-list-Hit ,pathway-Hit as well as total)
for FDR:-
FDR(pvals, qlevel = 0.05)
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools