curation
:
-
This slot contains three data.frames, one for drugs, tissues, and
-cells. Each contains two columns, the first with the unique identifier
-that is used between all PharmacoSet objects for this drug, and the
-second with the identifier used within the dataset. At this time there
-is no set method to find the unique identifiers between all PharmacoSets
-for arbitrary drugs, as much labour intensive curation has gone into
-carefully matching identifiers between datasets. However, these tables
-are used only by the intersecting function, and all other functions will
-function without this data, therefore for PharmacoSet objects created by
-users, we recommend just filling both columns with the identifiers used
-in the datasets, to allow for at least some matching to be done.
+
This slot contains three data.frames, one for sample
,
+treatment
, and tissue
. Each contains two
+columns, the first with the unique identifier that is used between all
+PharmacoSet objects for this drug, and the second with the identifier
+used within the dataset. At this time there is no set method to find the
+unique identifiers between all PharmacoSets for arbitrary drugs, as much
+labour intensive curation has gone into carefully matching identifiers
+between datasets. However, these tables are used only by the
+intersecting function, and all other functions will function without
+this data, therefore for PharmacoSet objects created by users, we
+recommend just filling both columns with the identifiers used in the
+datasets, to allow for at least some matching to be done.
-
sample
: data frame annotating all cell-lines
@@ -187,11 +212,14 @@
molecularProfiles
:
+
Either a:
-- List of
SummarizedExperiment
objects containing the
-molecular profiles of the cell lines, such as mutations, gene
-expressions, or copy number variations.
+- List of
SummarizedExperiment
objects
+-
+
MultiAssayExperiment
object
+containing the molecular profiles of the samples, such as mutations,
+gene expressions, or copy number variations.
The molecular profiles slot of a PharmacoSet object contains all the
molecular expression data profiled in the dataset. Each type of data is
kept in a separate SummarizedExperiment (SE) object, and they are all
@@ -206,7 +234,7 @@
diff --git a/articles/DetectingDrugSynergyAndAntagonism.html b/articles/DetectingDrugSynergyAndAntagonism.html
index a4c57a6..7e9ba31 100644
--- a/articles/DetectingDrugSynergyAndAntagonism.html
+++ b/articles/DetectingDrugSynergyAndAntagonism.html
@@ -22,11 +22,11 @@