In vladpetyuk/LewyBodies.SN.TopDown: What the package does (short line)

ProMex Unattributed

Low observation specied, no normalization

library("LewyBodies.SN.TopDown")
library("vp.misc")
library("msmsEDA")

Overview and Normalization

data(promex_unattributed)
data(promex_human_db)
# subset and transform
m <- m[,m$subject.type != 'control.2']
levels(m$subject.type) <- droplevels(m$subject.type)
# m <- m[rowSums(!is.na(m)) > 10,]
exprs(m) <- 1*!is.na(exprs(m))
#
dim(m)
image.lewy.iq(m)

PCA

counts.pca(m, facs=pData(m)[,"prepBatch",drop=F], snms=sampleNames(m))

Test Subject Groups

res <- eset_presence_absence(m, "subject.type", test='binom')
res$p.val.adj <- p.adjust(res$p.value)
sum(res$p.val.adj < 0.05, na.rm=T)
head(res[order(res$p.value),], 10)
hist(res$p.value, 50, col='lightgrey')
res[with(res, p.value < 0.01 & abs(effect) > 0.4),]

best <- rownames(res)[which.min(res$p.value)]
plot.lewy.count.feature(m, best)
plot.lewy.count.feature(m, 'KCRB.6')

hist(res$effect, 100)

vladpetyuk/LewyBodies.SN.TopDown documentation built on May 3, 2019, 6:15 p.m.