Get contrast(s) from SummarizedExperiment or DEGdata

Usage

get_contrast(object)

Arguments

object: A SummarizedExperiment or DEGdata object output from test_diff()

Value

Character, the existing contrast(s) in object, which is introduced in the test_diff step.

Examples

data(Silicosis_pg)
data <- Silicosis_pg
data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";")
# Make SummarizedExperiment
ecols <- grep("LFQ.", colnames(data_unique))
se <- make_se_parse(data_unique, ecols, mode = "delim", sep = "_")

filt <- filter_se(se, thr = 0, fraction = 0.3, filter_formula = ~ Reverse != "+" & Potential.contaminant!="+")
#> filter base on missing number is <= 0 in at least one condition.
#> filter base on missing number fraction < 0.3 in each row
#> filter base on giving formula 
norm <- normalize_vsn(filt)
#> vsn2: 8832 x 20 matrix (1 stratum). 
#> Please use 'meanSdPlot' to verify the fit.
imputed <- impute(norm, fun = "MinDet")
#> Imputing along margin 2 (samples/columns).
diff <- test_diff(imputed,type = "control", control = "PBS")
#> Tested contrasts: W10_vs_PBS, W2_vs_PBS, W4_vs_PBS, W6_vs_PBS, W9_vs_PBS
#> Strimmer's qvalue(t)
get_contrast(diff)
#> [1] "W10_vs_PBS" "W2_vs_PBS"  "W4_vs_PBS"  "W6_vs_PBS"  "W9_vs_PBS" 
diff <- test_diff(imputed,type = "manual", test = c("W9_vs_PBS","W6_vs_PBS"))
#> Tested contrasts: W9_vs_PBS, W6_vs_PBS
#> Strimmer's qvalue(t)
get_contrast(diff)
#> [1] "W6_vs_PBS" "W9_vs_PBS"