diff --git a/docs/404.html b/docs/404.html index 74c24f2b..4d97bd36 100644 --- a/docs/404.html +++ b/docs/404.html @@ -24,7 +24,7 @@ gDRutils - 1.3.7 + 1.3.8 + + + + + +
+
+
+

Set Unique Parental Identifiers

+ Source: R/standardize_MAE.R +
set_unique_cl_names.Rd
+
+ +
+

This function sets the CellLineName field in +colData to be unique by appending the clid in parentheses for duplicates.

+
+ +
+

Usage

+ 
set_unique_cl_names(se)
+
+ +
+

Arguments

+
se
+

A SummarizedExperiment object.

+ +
+
+

Value

+ + +

A SummarizedExperiment object with unique CellLineName in colData.

+
+ +
+

Examples

+ 
se <- SummarizedExperiment::SummarizedExperiment(
+  assays = list(counts = matrix(1:4, ncol = 2)),
+  colData = S4Vectors::DataFrame(CellLineName = c("ID1", "ID1"), clid = c("C1", "C2"))
+)
+se <- set_unique_cl_names(se)
+
+
+
+ + +
+ + + + + + + diff --git a/docs/reference/set_unique_drug_names.html b/docs/reference/set_unique_drug_names.html new file mode 100644 index 00000000..cb41cc9d --- /dev/null +++ b/docs/reference/set_unique_drug_names.html @@ -0,0 +1,107 @@ + +Set Unique Drug Names — set_unique_drug_names • gDRutils + Skip to contents + + +
+
+
+

Set Unique Drug Names

+ Source: R/standardize_MAE.R +
set_unique_drug_names.Rd
+
+ +
+

This function sets the DrugName, DrugName_2, and DrugName_3 fields in rowData +to be unique by appending the corresponding Gnumber, Gnumber_2, and Gnumber_3 in parentheses for duplicates.

+
+ +
+

Usage

+ 
set_unique_drug_names(se)
+
+ +
+

Arguments

+
se
+

A SummarizedExperiment object.

+ +
+
+

Value

+ + +

A SummarizedExperiment object with unique DrugName fields in rowData.

+
+ +
+

Examples

+ 
se <- SummarizedExperiment::SummarizedExperiment(
+  assays = list(counts = matrix(1:9, ncol = 3)),
+  rowData = S4Vectors::DataFrame(DrugName = c("DrugA", "DrugA", "DrugB"),
+  Gnumber = c("G1", "G2", "G5"),
+  DrugName_2 = c("DrugC", "DrugC", "DrugD"),
+  Gnumber_2 = c("G3", "G4", "G5")
+))
+se <- set_unique_drug_names(se)
+
+
+
+ + +
+ + + + + + + diff --git a/docs/reference/set_unique_identifiers.html b/docs/reference/set_unique_identifiers.html new file mode 100644 index 00000000..5a8974ab --- /dev/null +++ b/docs/reference/set_unique_identifiers.html @@ -0,0 +1,115 @@ + +Set Unique Identifiers in MultiAssayExperiment — set_unique_identifiers • gDRutils + Skip to contents + + +
+
+
+

Set Unique Identifiers in MultiAssayExperiment

+ Source: R/standardize_MAE.R +
set_unique_identifiers.Rd
+
+ +
+

This function sets the CellLineName in colData and DrugName fields in rowData +to be unique for each SummarizedExperiment in a MultiAssayExperiment.

+
+ +
+

Usage

+ 
set_unique_identifiers(mae)
+
+ +
+

Arguments

+
mae
+

A MultiAssayExperiment object.

+ +
+
+

Value

+ + +

A MultiAssayExperiment object with unique identifiers.

+
+ +
+

Examples

+ 
se1 <- SummarizedExperiment::SummarizedExperiment(
+  assays = list(counts = matrix(1:4, ncol = 2)),
+  colData = S4Vectors::DataFrame(parental_identifier = c("ID1", "ID1"), clid = c("C1", "C2")),
+  rowData = S4Vectors::DataFrame(DrugName = c("DrugA", "DrugA"), Gnumber = c("G1", "G2"))
+)
+rownames(SummarizedExperiment::colData(se1)) <- c("cl1", "cl2")
+rownames(SummarizedExperiment::rowData(se1)) <- c("g1", "g")
+se2 <- SummarizedExperiment::SummarizedExperiment(
+  assays = list(counts = matrix(5:8, ncol = 2)),
+  colData = S4Vectors::DataFrame(parental_identifier = c("ID2", "ID2"), clid = c("C3", "C4")),
+  rowData = S4Vectors::DataFrame(DrugName = c("DrugB", "DrugB"), Gnumber = c("G3", "G4"))
+)
+rownames(SummarizedExperiment::colData(se2)) <- c("cl3", "cl4")
+rownames(SummarizedExperiment::rowData(se2)) <- c("g3", "g4")
+mae <- MultiAssayExperiment::MultiAssayExperiment(experiments = list(se1 = se1, se2 = se2))
+mae <- set_unique_identifiers(mae)
+
+
+
+ + +
+ + + + + + + diff --git a/docs/reference/shorten_normalization_type_name.html b/docs/reference/shorten_normalization_type_name.html index 816e6d64..dcaa3abf 100644 --- a/docs/reference/shorten_normalization_type_name.html +++ b/docs/reference/shorten_normalization_type_name.html @@ -10,7 +10,7 @@ gDRutils - 1.3.7 + 1.3.8