bootstrapAUC {TBSignatureProfiler} | R Documentation |
Run bootstrapping of the AUC and derive the p-value for a 2-sample t-test for all signatures tested on a given dataset.
bootstrapAUC( SE_scored, annotationColName, signatureColNames, num.boot = 100, pb.show = TRUE )
SE_scored |
a |
annotationColName |
a character string giving the column name in
|
signatureColNames |
a vector of column names in the
|
num.boot |
integer. The number of times to bootstrap the data. The
default is |
pb.show |
logical for whether to show a progress bar while running code.
The default is |
A list of length 5 returning a vector of p-values for a 2-sample
t-test, bootstrapped AUC values, an AUC value for using all scored values
for all signatures specified in signatureColNames
,
and values for the lower and upper bounds of a bootstrapped AUC confidence
interval using pROC::roc()
.
# Run signature profiling choose_sigs <- TBsignatures[1] prof_indian <- runTBsigProfiler(TB_indian, useAssay = "logcounts", algorithm = "ssGSEA", combineSigAndAlgorithm = TRUE, signatures = choose_sigs, parallel.sz = 1) # Bootstrapping booted <- bootstrapAUC(SE_scored = prof_indian, annotationColName = "label", signatureColNames = names(choose_sigs), num.boot = 5) booted