slicing {GenomicDataCommons} | R Documentation |
This function returns a BAM file representing reads overlapping regions specified either as chromosomal regions or as gencode gene symbols.
slicing(uuid, regions, symbols, destination = tempfile(), overwrite = FALSE, progress = interactive(), token = NULL, legacy = FALSE)
uuid |
character(1) identifying the BAM file resource |
regions |
character() vector describing chromosomal regions,
e.g., |
symbols |
character() vector of gencode gene symbols, e.g.,
|
destination |
character(1) default |
overwrite |
logical(1) default FALSE can destination be overwritten? |
progress |
logical(1) default |
token |
character(1) security token allowing access to restricted data. Almost all BAM data is restricted, so a token is usually required. See https://gdc-docs.nci.nih.gov/API/Users_Guide/Authentication_and_Authorization/. |
legacy |
logical(1) whether or not to use the "legacy" archive, containing older, non-harmonized data. |
character(1) destination to the downloaded BAM file
slicing("df80679e-c4d3-487b-934c-fcc782e5d46e", regions="chr17:75000000-76000000", token=gdc_token())