predictTargetingDrugs {cTRAP} | R Documentation |
Identify compounds that may target the phenotype associated with a user-provided differential expression profile by comparing such against a correlation matrix of gene expression and drug sensitivity.
predictTargetingDrugs(diffExprGenes, expressionDrugSensitivityCor, method = c("spearman", "pearson", "gsea"), geneSize = 150, isDrugActivityDirectlyProportionalToSensitivity = NULL)
diffExprGenes |
Numeric: named vector of differentially expressed genes whose names are gene identifiers and respective values are a statistic that represents significance and magnitude of differentially expressed genes (e.g. t-statistics) |
expressionDrugSensitivityCor |
Matrix: correlation matrix of gene
expression (rows) and drug sensitivity (columns) across cell lines.
Pre-prepared gene expression and drug sensitivity associations are
available to download using
|
method |
Character: comparison methods to run ( |
geneSize |
Number: top and bottom number of differentially expressed
genes for gene set enrichment (only used if |
isDrugActivityDirectlyProportionalToSensitivity |
Boolean: are the values used for drug activity directly proportional to drug sensitivity? See details. |
If isDrugActivityDirectlyProportionalToSensitivity
is set to
NULL
(as by default), the attribute
isDrugMetricDirectlyProportionalToSensitivity
on the object passed
as argument expressionDrugSensitivityCor
is used (objects obtained
via loadExpressionDrugSensitivityAssociation
have the
mentioned attribute set).
Data table with correlation or GSEA results comparing differential expression values against gene expression and drug sensitivity associations
Weighted connectivity scores (WTCS) are calculated when method
= "gsea"
(https://clue.io/connectopedia/cmap_algorithms).
Other functions related with the prediction of targeting drugs: loadExpressionDrugSensitivityAssociation
,
plot.referenceComparison
,
plotTargetingDrugsVSsimilarPerturbations
# Example of a differential expression profile data("diffExprStat") # Load expression and drug sensitivity association derived from GDSC data gdsc <- loadExpressionDrugSensitivityAssociation("GDSC 7") # Predict targeting drugs on a differential expression profile predictTargetingDrugs(diffExprStat, gdsc)