clinical rnaseq

library(lsa)
list1 = c("g1","g2","g3","g4")
list2 = c("g3","g4","g5","g6","g1")

u = union(list1,list2)
u
a = as.numeric(u %in% list1)
a
b = as.numeric(u %in% list2)
b
lsa::cosine(a,b)


# with up or downregulation
list1 = c("g1-u","g2-d","g3-d","g4-u","g5-u")
list2 = c("g3-d","g4-u","g5-d","g6-u","g1-d")
u = union(list1,list2)
u
a = as.numeric(u %in% list1)
a
b = as.numeric(u %in% list2)
b
lsa::cosine(a,b)


# standardizing values like Harmonizome
genes = c("MKI67", "CCNE1", "TP53", "KPNA6")
log2foldchange = c(2.5, 3, -2, 0.1)
pvalue = c(0.0001, 0.003, 0.0000057, 0.2) # the pvalues associated with each log2 fold change
logged = -log10(pvalue)
stdvals = logged * sign(log2foldchange)  # change sign of each pvalue to indicate if gene is up or down regulated
stdvals