NCI Genomic Data Commons Access

slicing

R Documentation

Query GDC for data slices

Description

This function returns a BAM file representing reads overlapping regions specified either as chromosomal regions or as gencode gene symbols.

Usage

slicing(
  uuid,
  regions,
  symbols,
  destination = file.path(tempdir(), paste0(uuid, ".bam")),
  overwrite = FALSE,
  progress = interactive(),
  token = gdc_token()
)

Arguments

`uuid`	character(1) identifying the BAM file resource
`regions`	character() vector describing chromosomal regions, e.g., `c("chr1", "chr2:10000", "chr3:10000-20000")` (all of chromosome 1, chromosome 2 from position 10000 to the end, chromosome 3 from 10000 to 20000).
`symbols`	character() vector of gencode gene symbols, e.g., `c("BRCA1", "PTEN")`
`destination`	character(1) default `tempfile()` file path for BAM file slice
`overwrite`	logical(1) default FALSE can destination be overwritten?
`progress`	logical(1) default `interactive()` should a progress bar be used?
`token`	character(1) security token allowing access to restricted data. Almost all BAM data is restricted, so a token is usually required. See https://docs.gdc.cancer.gov/Data/Data_Security/Data_Security/#authentication-tokens.

Details

This function uses the Genomic Data Commons "slicing" API to get portions of a BAM file specified either using "regions" or using HGNC gene symbols.

Value

character(1) destination to the downloaded BAM file

Examples

## Not run: 
 slicing("df80679e-c4d3-487b-934c-fcc782e5d46e",
        regions="chr17:75000000-76000000",
        token=gdc_token())

# Get 10 BAM files.
bamfiles = files() |> 
           filter(data_format=='BAM') |>
           results(size=10) |> ids()

# Current alignments at the GDC are to GRCh38
library('TxDb.Hsapiens.UCSC.hg38.knownGene')
all_genes = genes(TxDb.Hsapiens.UCSC.hg38.knownGene)

first3genes = all_genes[1:3]
# remove strand info
strand(first3genes) = '*'

# We can get our regions easily now
as.character(first3genes)

# Use parallel downloads to speed processing
library(BiocParallel)
register(MulticoreParam())

fnames = bplapply(bamfiles, slicing, overwrite = TRUE,
                regions=as.character(first3genes))

# 10 BAM files
fnames

library(GenomicAlignments)
lapply(unlist(fnames), readGAlignments)


## End(Not run)

Bioconductor/GenomicDataCommons documentation built on Oct. 31, 2024, 7 a.m.