all-functions: SomaticCancerAlterations functions

In juliangehring/SomaticCancerAlterations: Somatic Cancer Alterations

Description

Functions to interact with the 'SomaticCancerAlterations' datasets.

Usage

scaMetadata()

scaListDatasets()

scaLoadDatasets(names, merge = FALSE)

Arguments

names	Character vector with data set name(s) to load. The names are the same as returned from 'scaListDatasets()'.
merge	Logical. Should the results be a merged 'GRanges' object with data of all studies (TRUE), or a 'GRangesList' with one list element per dataset (FALSE [default]).

Details

The 'sca_load_dataset' function makes it easy to load the data of a study directly into a variable.

Value

scaMetadata	A data frame summarizing the available data sets, with rows corresponding to data sets.
scaListDatasets	A character vector with all available study names.
sca_load_dataset	A GRangesList or GRanges objecs, depending on the 'merge' argument.

References

https://tcga-data.nci.nih.gov/tcga/

https://wiki.nci.nih.gov/display/TCGA/TCGA+Data+Primer

https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/

See Also

SomaticCancerAlterations-data

Examples

meta_data = scaMetadata()
head(meta_data)

all_datasets = scaListDatasets()
head(all_datasets)

grl = scaLoadDatasets(all_datasets[1], merge = FALSE)

gr = scaLoadDatasets(all_datasets[1], merge = TRUE)

juliangehring/SomaticCancerAlterations documentation built on Jan. 1, 2021, 7:12 a.m.