| plot_p_hist {DEP} | R Documentation |
plot_p_hist generates a p value histogram.
plot_p_hist(dep, adjusted = FALSE, wrap = FALSE)
dep |
SummarizedExperiment,
Data object for which differentially enriched proteins are annotated
(output from |
adjusted |
Logical(1), Whether or not to use adjusted p values. |
wrap |
Logical(1), Whether or not to display different histograms for the different contrasts. |
A histogram (generated by ggplot).
# Load example
data <- UbiLength
data <- data[data$Reverse != "+" & data$Potential.contaminant != "+",]
data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";")
# Make SummarizedExperiment
columns <- grep("LFQ.", colnames(data_unique))
exp_design <- UbiLength_ExpDesign
se <- make_se(data_unique, columns, exp_design)
# Filter, normalize and impute missing values
filt <- filter_missval(se, thr = 0)
norm <- normalize_vsn(filt)
imputed <- impute(norm, fun = "MinProb", q = 0.01)
# Test for differentially expressed proteins
diff <- test_diff(imputed, "control", "Ctrl")
dep <- add_rejections(diff, alpha = 0.05, lfc = 1)
# Plot p value histogram
plot_p_hist(dep)
plot_p_hist(dep, wrap = TRUE)