lp2
commented
2 years ago Hello,
thank you for the report. Ricard (cc-d) has folded PEER into the multi-omics factor analysis (MOFA) framework as described below - we recommend using this going forward, as it is properly supported, and it may resolve your issues.
Leo
From Ricard:
Running MOFA (https://github.com/bioFAM/MOFA2) with one view is effectively PEER. We have also added functionalities and visualisations to interpret the factors before regressing them out for eQTL mapping or any other downstream analysis.
I’ve built a wrapper here: https://github.com/bioFAM/PEER
Let me know if you have any questions. We have a Slack channel where I provide individualised help. The link is in the MOFA2 github.
We have not made the official release yet as we would like to get some feedback how this is working and how intuitive this is. Please let me know about your experience
Best, Ricard.
On Fri, Feb 18, 2022 at 12:59 PM hust-yyan @.***> wrote:
Hello, I encountered the following bug when running R-peer again [image: image] https://user-images.githubusercontent.com/54279739/154687130-c40201e1-5ddd-40f3-9a45-994e7fb4c63d.png this is my code: library(peer) load("/data1/shiyan_data/plasma.miRNA.eqtl.RData") model = PEER() PEER_setPhenoMean(model,as.matrix(t(counts)))
covs<-sampleinfo[,c("Sex","Age","BMI","Smoking","hypertension","hyperlipidemia","Diabetes")] covs<-apply(covs,2,as.numeric) rownames(covs)<-sampleinfo$ID PEER_setCovariates(model, as.matrix(covs)) PEER_setAdd_mean(model, TRUE) PEER_update(model)
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hust-yyan
Hello, I encountered the following bug when running R-peer again
this is my code:
library(peer)
load("/data1/shiyan_data/plasma.miRNA.eqtl.RData")
model = PEER()
PEER_setPhenoMean(model,as.matrix(t(counts)))
covs<-sampleinfo[,c("Sex","Age","BMI","Smoking","hypertension","hyperlipidemia","Diabetes")]
covs<-apply(covs,2,as.numeric)
rownames(covs)<-sampleinfo$ID
PEER_setCovariates(model, as.matrix(covs))
PEER_setAdd_mean(model, TRUE)
PEER_update(model)