find.DE.features {iDOS} | R Documentation |
find.DE.features
Description
Funtion to identify differentially expressed/variable features between Tumour (T) and Normal (N) profiles
Usage
find.DE.features(
exp.data.T = NULL,
exp.data.N = NULL,
feature.ids = NULL,
test.name = "t.test"
)
Arguments
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 |
Value
Feature by cancer type matrix of log2 fold change (T vs N) and adjusted P values. P values are estimated through test.name
Author(s)
Syed Haider
See Also
Examples
# 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"
);
[Package iDOS version 1.0.1 Index]