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Commit f27f7a31 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Tweak cutoffs for var.genes

parent 81f06892
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...@@ -53,8 +53,8 @@ tryCatch({ ...@@ -53,8 +53,8 @@ tryCatch({
rm(sc10x.Group) rm(sc10x.Group)
#re-detect variable genes in Epi + St subsets #re-detect variable genes in Epi + St subsets
sc10x.Group.Epi <- FindVariableGenes(object=sc10x.Group.Epi,mean.function=ExpMean,dispersion.function=LogVMR,x.low.cutoff=0.075,x.high.cutoff=4,y.cutoff=0.075,do.plot=FALSE) sc10x.Group.Epi <- FindVariableGenes(object=sc10x.Group.Epi,mean.function=ExpMean,dispersion.function=LogVMR,x.low.cutoff=0.075,x.high.cutoff=3.5,y.cutoff=0.5,do.plot=FALSE)
sc10x.Group.St <- FindVariableGenes(object=sc10x.Group.St,mean.function=ExpMean,dispersion.function=LogVMR,x.low.cutoff=0.075,x.high.cutoff=4,y.cutoff=0.075,do.plot=FALSE) sc10x.Group.St <- FindVariableGenes(object=sc10x.Group.St,mean.function=ExpMean,dispersion.function=LogVMR,x.low.cutoff=0.075,x.high.cutoff=3.5,y.cutoff=0.5,do.plot=FALSE)
genes.var.NoStress.Epi <- sc10x.Group.Epi@var.genes genes.var.NoStress.Epi <- sc10x.Group.Epi@var.genes
genes.var.NoStress.St <- sc10x.Group.St@var.genes genes.var.NoStress.St <- sc10x.Group.St@var.genes
......
...@@ -73,7 +73,7 @@ dev.off() ...@@ -73,7 +73,7 @@ dev.off()
sc10x.Group.FilteredCellCount <- length(sc10x.Group@data@Dimnames[[2]]) sc10x.Group.FilteredCellCount <- length(sc10x.Group@data@Dimnames[[2]])
sc10x.Group.FilteredGeneCount <- length(sc10x.Group@data@Dimnames[[1]]) sc10x.Group.FilteredGeneCount <- length(sc10x.Group@data@Dimnames[[1]])
sc10x.Group@data <- sc10x.Group@data[!rownames(sc10x.Group@data) %in% mito.genes,] sc10x.Group@data <- sc10x.Group@data[!rownames(sc10x.Group@data) %in% mito.genes,]
sc10x.Group <- FindVariableGenes(object=sc10x.Group,mean.function=ExpMean,dispersion.function=LogVMR,x.low.cutoff=0.075,x.high.cutoff=4,y.cutoff=0.075,do.plot=FALSE) sc10x.Group <- FindVariableGenes(object=sc10x.Group,mean.function=ExpMean,dispersion.function=LogVMR,x.low.cutoff=0.075,x.high.cutoff=3.5,y.cutoff=0.5,do.plot=FALSE)
genes.var <- sc10x.Group@var.genes genes.var <- sc10x.Group@var.genes
if (opt$cc==TRUE){ if (opt$cc==TRUE){
gc() gc()
......
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