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

MS-Align

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

Overview and Normalization

data(msal_human_default)
# subset
m <- m[rowSums(exprs(m) > 0) > 10,]
#
dim(m)
image.lewy.counts(m)

PCA

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

Test prepBatch

library("msmsTests")
res <- msms.glm.qlll(m, 
                     "y ~ prepBatch + 1",
                     "y ~ 1",
                     div=colSums(exprs(m)))
res$p.val.adj <- p.adjust(res$p.value)
sum(res$p.val.adj < 0.05)
sum(res$p.val.adj < 0.05)/nrow(res)
hist(res$p.value, 50, col='lightgrey')

Test Subject Groups

res <- msms.glm.qlll(m, 
                     "y ~ subject.type + match.group",
                     "y ~ match.group",
                     div=colSums(exprs(m)))
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')

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

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