test_diff: Differential enrichment test

In squirrelandr/DEP: Differential Enrichment analysis of Proteomics data

Description

test_diff performs a differential enrichment test based on protein-wise linear models and empirical Bayes statistics using limma.

Usage

test_diff(se, type = c("control", "all", "manual"), control = NULL,
  test = NULL, design_formula = formula(~0 + condition))

Arguments

se	SummarizedExperiment, Proteomics data (output from make_se() or make_se_parse()). It is adviced to first remove proteins with too many missing values using filter_missval(), normalize the data using normalize_vsn() and impute remaining missing values using impute().
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.

Value

A SummarizedExperiment object containing FDR estimates of differential expression.

Examples

# 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))

squirrelandr/DEP documentation built on May 7, 2019, 9:31 a.m.