blcaOutputExamples: TCGAretriever Examples

In dami82/TCGAretriever: Retrieve Genomic and Clinical Data from CBioPortal Including TCGA Data

TCGAretriever Examples

Description

A list of objects including examples of the output returned by different 'TCGAretriever' functions. The objects were obtained from the '"blca_tcga"' study (bladder cancer).

Usage

data(blcaOutputExamples)

Format

A list including 7 elements.

exmpl_1

data.frame (dimensions: 10 by 13). Sample output of the 'get_cancer_studies()' function.

exmpl_2

data.frame (dimensions: 10 by 5). Sample output of the 'get_cancer_types()' function.

exmpl_3

data.frame (dimensions: 9 by 5). Sample output of the 'get_case_lists()' function.

exmpl_4

list including 9 elements. Sample output of the 'expand_cases()' function.

exmpl_5

data.frame (dimensions: 10 by 94). Sample output of the 'get_clinical_data()' function.

exmpl_6

data.frame (dimensions: 9 by 8). Sample output of the 'get_genetic_profiles()' function.

exmpl_7

data.frame (dimensions: 10 by 3). Sample output of the 'get_gene_identifiers()' function.

exmpl_8

data.frame (dimensions: 2 by 10). Sample output of the 'get_molecular_data()' function.

exmpl_9

data.frame (dimensions: 6 by 27). Sample output of the 'get_mutation_data()' function.

Details

The object was built using the following lines of code. blcaOutputExamples <- list( exmpl_1 = head(get_cancer_studies(), 10), exmpl_2 = head(get_cancer_types(), 10), exmpl_3 = head(get_case_lists("blca_tcga"), 10) , exmpl_4 = expand_cases("blca_tcga"), exmpl_5 = head(get_clinical_data("blca_tcga"), 10), exmpl_6 = head(get_genetic_profiles("blca_tcga") , 10), exmpl_7 = head(get_gene_identifiers(), 10), exmpl_8 = get_molecular_data(case_list_id = 'blca_tcga_3way_complete', gprofile_id = 'blca_tcga_rna_seq_v2_mrna', glist = c("TP53", "E2F1"))[, 1:10], exmpl_9 = head(get_mutation_data(case_list_id = 'blca_tcga_sequenced', gprofile_id = 'blca_tcga_mutations', glist = c('TP53', 'PTEN'))))

Examples

data(blcaOutputExamples)
blcaOutputExamples$exmpl_1

dami82/TCGAretriever documentation built on Feb. 2, 2024, 12:06 p.m.