View source: R/find.DE.features.R
find.DE.features | R Documentation |
Funtion to identify differentially expressed/variable features between Tumour (T) and Normal (N) profiles
find.DE.features(
exp.data.T = NULL,
exp.data.N = NULL,
feature.ids = NULL,
test.name = "t.test"
)
exp.data.T |
Feature by sample mRNA abundance matrix; tumour samples |
exp.data.N |
Feature by sample mRNA abundance matrix; normal/baseline samples |
feature.ids |
Vector of features to be used to estimate correlation |
test.name |
Specify the statistical test name (exactly as it appears in R). Supported tests are |
Feature by cancer type matrix of log2 fold change (T vs N) and adjusted P values. P values are estimated through test.name
Syed Haider
t.test
,
wilcox.test
,
var.test
# load test data
x <- get.test.data(data.types = c("mRNA.T", "mRNA.N"));
# list of features to be assessed for differential expression
feature.ids <- rownames(x$mRNA.T$BLCA);
DE.results <- find.DE.features(
exp.data.T = x$mRNA.T,
exp.data.N = x$mRNA.N,
feature.ids = feature.ids,
test.name = "t.test"
);
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