Lara Urban IHW question 2018-11-18
18 November 2018
1 Setup
library("IHW")
library("ggplot2")2 Lara’s post
pfin <- read.table('pfins.tsv', sep='\t', header=TRUE, row.names = 1)
ihwRes <- ihw(p ~ var, data = pfin, alpha = 0.1)
pfin$padj <- adj_pvalues(ihwRes)
pfin$BH <- p.adjust(pfin$p, method = "BH")
head(pfin)## p var padj BH
## 1 0.08518485 0.04687183 0.7391697 0.7391697
## 2 0.29819847 0.03476625 0.8619217 0.8619217
## 3 0.21340210 0.03651571 0.8320083 0.8320083
## 4 0.52053214 0.11713521 0.9242342 0.9242342
## 5 0.50901341 0.34885276 0.9219028 0.9219028
## 6 0.43508199 0.09018223 0.9014622 0.9014622plot(ihwRes)
ggplot(aes(x = rank(var), y = -log10(p)), data=pfin) + geom_hex(bins = 100) + ylab(expression(-log[10]~p))
3 Histogram of p and Schweder-Spjøtvoll plot
ggplot(pfin, aes(x = p)) + geom_histogram(binwidth = 0.005, boundary = 0)
There seems to be a small enrichment of small p-values; we can also verify this using the Schweder-Spjøtvoll plot, see the orange line.
metap::schweder(pfin$p, drawline = c("ls", "bh"),
ls.col = "red", ls.lty = 1, ls.control = list(frac = 1/3),
bh.col = "blue")
Also the BH method indicates that there are a few discoveries to be made, but only with FDR of 40% or higher.
ggplot(dplyr::filter(pfin, BH < 1), aes(x = BH)) +
geom_histogram(binwidth = 0.01, boundary = 0)
4 Stratification by var
ggplot(pfin, aes(x = var)) + geom_histogram(binwidth = 0.01)
ggplot(pfin, aes(x = p)) + geom_histogram(binwidth = 0.040, boundary = 0) +
facet_wrap(~ groups_by_filter(pfin$var, 8), nrow = 2)
There seems to be a weak trend that the enrichment of small p-values is strongest for small var. Perhaps this could also be a normalization / data preprocessing artefact?
5 Conclusion
var is not a strong covariate. You’ll have to search for others.
6 Session info
devtools::session_info()## ─ Session info ────────────────────────────────────────────────────────────
## setting value
## version R version 3.5.1 (2018-07-02)
## os macOS 10.14.1
## system x86_64, darwin15.6.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Europe/Berlin
## date 2018-11-18
##
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