Description Usage Arguments Value Examples
test_diff
performs a differential enrichment test based on
protein-wise linear models and empirical Bayes
statistics using limma. False Discovery Rates are estimated
using fdrtool.
1 2 |
se |
SummarizedExperiment,
Proteomics data (output from |
type |
"control", "all" or "manual", The type of contrasts that will be tested. This can be all possible pairwise comparisons ("all"), limited to the comparisons versus the control ("control"), or manually defined contrasts ("manual"). |
control |
Character(1), The condition to which contrasts are generated if type = "control" (a control condition would be most appropriate). |
test |
Character, The contrasts that will be tested if type = "manual". These should be formatted as "SampleA_vs_SampleB" or c("SampleA_vs_SampleC", "SampleB_vs_SampleC"). |
design_formula |
Formula, Used to create the design matrix. |
A SummarizedExperiment object containing fdr estimates of differential expression.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | # 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")
diff <- test_diff(imputed, "manual",
test = c("Ubi4_vs_Ctrl", "Ubi6_vs_Ctrl"))
# Test for differentially expressed proteins with a custom design formula
diff <- test_diff(imputed, "control", "Ctrl",
design_formula = formula(~ 0 + condition + replicate))
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