Nothing
StabPlotData <-
function(mGSZobj,rank.vector,sample.perm.data=FALSE){
# sample.perm.data: TRUE if sample perm data is to be plotted instead of gene data
########################################
## Testing that data sizes are correct #
########################################
gene.sets <- mGSZobj$gene.sets
expr.data <- mGSZobj$expr.data
expr.dat.sz <- dim(expr.data)
perm.number <- mGSZobj$perm.number
sample.labels <- mGSZobj$sample.labels
flip.gene.sets <- mGSZobj$flip.gene.sets
select <- mGSZobj$select
is.log <- mGSZobj$is.log
gene.perm <- mGSZobj$gene.perm.log
min.cl.sz <- mGSZobj$min.cl.sz
other.methods <- mGSZobj$other.methods
pre.var <- mGSZobj$pre.var
wgt1 <- mGSZobj$wgt1
wgt2 <- mGSZobj$wgt2
var.constant <- mGSZobj$var.constant
start.val <- mGSZobj$start.val
geneset.classes <- colnames(gene.sets)
num.classes <- dim(gene.sets)[2]
num.genes <- dim(expr.data)[1]
geneset.class.sizes <- colSums(gene.sets)
#require(limma)
#require(Biobase)
if(select=="FC"){
tmp.expr.data = diff.FC.perm(expr.data, sample.labels, perm.number)
}
else
tmp = diff_c_perm(expr.data, sample.labels, perm.number)
if(select=="T-score"){
tmp.expr.data = tmp$t_scores}
if(select=="P-value"){
tmp.expr.data=tmp$p_values}
diff.expr.dat.sz <- dim(tmp.expr.data)
if(gene.perm==TRUE & other.methods==TRUE){
gene.sets.stb <- as.vector(mGSZobj$gene.perm$mGSZ[,1][rank.vector])
}
if(gene.perm==TRUE & other.methods==FALSE){
gene.sets.stb <- as.vector(mGSZobj$mGSZ.gene.perm[,1][rank.vector])
}
if(gene.perm==TRUE & sample.perm.data==TRUE & other.methods==TRUE){
gene.sets.stb <- as.vector(mGSZobj$sample.perm$mGSZ[,1][rank.vector])
}
if(gene.perm==TRUE & sample.perm.data==TRUE & other.methods==FALSE){
gene.sets.stb <- as.vector(mGSZobj$mGSZ.sample.perm[,1][rank.vector])
}
if(gene.perm==FALSE & other.methods==TRUE){
gene.sets.stb <- as.vector(mGSZobj$mGSZ[,1][rank.vector])
}
if(gene.perm==FALSE & other.methods==FALSE){
gene.sets.stb <- as.vector(mGSZobj$mGSZ[,1][rank.vector])
}
## mGSZ for positive data ####
#############################
pos.scores <- mGSZ.test.score.stb2(gene.sets.stb=gene.sets.stb,expr.data=tmp.expr.data[,1], gene.sets,wgt1=wgt1,wgt2=wgt2,pre.var=pre.var,var.constant=var.constant,start.val=start.val)
mGSZ.up <- pos.scores$mGSZ.up
## mGSZ for col randomized data ###
##################################
col.perm.mGSZ <- matrix(0, diff.expr.dat.sz[2]-1, num.classes)
mGSZ.cperm.up <- vector("list",length(rank.vector))
for( k in 1:(diff.expr.dat.sz[2]-1)){
tmp <- mGSZ.test.score.stb3(gene.sets.stb=gene.sets.stb,expr.data=tmp.expr.data[,k+1], gene.sets=gene.sets,wgt1=wgt1,wgt2=wgt2,pre.var=pre.var,var.constant=var.constant,start.val=start.val)
mGSZ.cperm.up[[k]] <- tmp$mGSZ.up
}
out <- list(positive.prof.up = mGSZ.up, perm.data = mGSZ.cperm.up, expr.data = expr.data, gene.sets = gene.sets, perm.number = perm.number,rank.vector=rank.vector,gene.sets.stb=gene.sets.stb)
if(gene.perm==TRUE){
mGSZ.rperm.up <- vector("list",length(rank.vector))
row.permuted.data <- replicate(perm.number,sample(tmp.expr.data[,1], num.genes, replace=FALSE))
unique.perm <- unique(t(row.permuted.data))
row.permuted.data <- t(unique.perm)
for(i in 1:perm.number){
res <- mGSZ.test.score.stb4(gene.sets.stb=gene.sets.stb, expr.data=row.permuted.data[,i],gene.sets=gene.sets,Z_var1=pos.scores$var.attributes$Z_var1, Z_var2=pos.scores$var.attributes$Z_var2, Z_mean1=pos.scores$var.attributes$Z_mean1, Z_mean2=pos.scores$var.attributes$Z_mean2,class_size_index1=pos.scores$var.attributes$class_size_index1, class_size_index2=pos.scores$var.attributes$class_size_index2,start.val)
mGSZ.rperm.up[[i]] <- res$mGSZ.up
}
out <- list(positive.prof.up = mGSZ.up, perm.data = mGSZ.rperm.up, expr.data = expr.data, gene.sets = gene.sets, perm.number = perm.number,rank.vector=rank.vector,gene.sets.stb=gene.sets.stb)
if(gene.perm==TRUE & sample.perm.data==TRUE){
out <- list(positive.prof.up = mGSZ.up, perm.data = mGSZ.cperm.up, expr.data = expr.data, gene.sets = gene.sets, perm.number = perm.number,rank.vector=rank.vector,gene.sets.stb=gene.sets.stb)
}
}
out
}
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