datasets: Functions to access/manage dataset level data

In ShixiangWang/coco: Interactive Cancer Explorer

Functions to access/manage dataset level data

Description

A dataset contains a specified type of data, a cohort contains a list of datasets. TODO: ENSEMBL IDs and Hugo Symbol will be supported and the can exchange automatically.

Usage

datasets(id, verbose = FALSE)

dataset_info(id, cohort, verbose = FALSE)

dataset_query_idx(id, cohort, verbose = FALSE)

dataset_load(id, cohort, subset = NULL, select = NULL, verbose = FALSE, ...)

Arguments

id	A dataset ID.
verbose	Whether to print extra information.
cohort	A cohort ID.
subset	A expression to subset the dataset.
select	A vector of column names or numbers to keep, drop the rest.
...	other parameters passing to data.table::fread().

Functions

• dataset_info: Show information of a specified dataset

• dataset_query_idx: Query index information for a dataset

• dataset_load: Load data from specified dataset

Examples

datasets("example_TCGA_LAML")

dataset_info("example_TCGA_LAML_MAF", "example_TCGA_LAML")

dataset_query_idx("example_TCGA_LAML_MAF", "example_TCGA_LAML")
dataset_query_idx("example_TCGA_LAML_gene_expr_HTSeq_count", "example_TCGA_LAML")

dataset_load("example_TCGA_LAML_gene_expr_HTSeq_count", "example_TCGA_LAML")
dataset_load("example_TCGA_LAML_gene_expr_HTSeq_count", "example_TCGA_LAML", select = 1:3)
dataset_load("example_TCGA_LAML_gene_expr_HTSeq_count", "example_TCGA_LAML",
  select = c("Ensembl_ID", "TCGA-AB-2918-03A"), subset = Ensembl_ID == "ENSG00000251400"
)

ShixiangWang/coco documentation built on July 9, 2022, 4:43 a.m.