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This vignette highlights a simple example workflow for performing
power analysis for ST data using the PoweREST
R package. A
detailed version can be found on PoweREST GitHub page.
Once installed, PoweREST
can be simply
loaded (along with the required packages) as follows:
#load ST data in R by Seurat:
#here we load the pancreatic cancer data which is available on GitHub page
three_areas <- readRDS("your path to/GSE233293_scMC.all.3areas.final")
Idents(three_areas)
#Levels: Peri Juxta Epi
SeuratObject_splitlist<-Seurat::SplitObject(three_areas, split.by = "ident")
#split the ST data into three areas
for (i in 1:length(SeuratObject_splitlist)) {
SeuratObject_splitlist[[i]][['Condition']]<-ifelse(SeuratObject_splitlist[[i]][['Type']]=='LG','LG','HR')
}
for (i in 1:length(SeuratObject_splitlist)) {
Seurat::Idents(SeuratObject_splitlist[[i]])<-"Condition"
}
# Take Peri area for example for downstream analysis
Peri<-SeuratObject_splitlist$Peri
result<-PoweREST(Peri,cond='Condition',replicates=5,spots_num=80,iteration=100)
#---For test, try this first
#PoweREST(Peri,cond='Condition',replicates=5,spots_num=80,iteration=2)
#---To get faster, try this
#devtools::install_github('immunogenomics/presto')
# For example, use the Student's t-test
result2<-PoweREST(Peri,cond='Condition',replicates=5,spots_num=80,iteration=100,test.use="t")
Users can also use PoweREST_gene and PoweREST_subset to perform the power estimation upon one gene or a subset of genes. ### PoweREST_gene
#Fit the power surface for sample size=5 in each arm
b<-fit_powerest(result$power,result$avg_logFC,result$avg_PCT)
# Fit the local power surface of avg_log2FC_abs between 1 and 2
avg_log2FC_abs_1_2<-dplyr::filter(power,avg_log2FC_abs>1 & avg_log2FC_abs<2)
# Fit the model
bst<-fit_XGBoost(power$power,avg_log2FC=power$avg_log2FC_abs,avg_PCT=power$mean_pct,replicates=power$sample_size)
# Make predictions
pred<-pred_XGBoost(bst,n.grid=30,xlim=c(0,1.5),ylim=c(0,0.1),replicates=3)
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.