Import bigwig files from the UCSC Genome Browser

Source: R/import_ucsc_bigwigs.R

Import, preprocess, merge, and save data from UCSC Genome Browser tracks.

import_ucsc_bigwigs(
  query_dat,
  bigwig_metadata,
  full_data = TRUE,
  xlims = NULL,
  save_path = tempfile(),
  force_new = FALSE,
  nThread = 1,
  verbose = TRUE
)

Arguments

query_dat

data.table or GRanges containing genomic coordinates to query the UCSC tracks with.

bigwig_metadata

Metadata table with at least the following two columns:

  • "name"Unique name of the file.

  • "data_link"URL to UCSC genome browser bigwig file.

full_data

Whether to download the full data (genomic ranges of all sequence reads) as opposed to a reduced representation of the data as a single vector (i.e. the aggregated reads "score"). Setting full_data=TRUE is necessary for creating histograms and density plots.

xlims

Min/max positions to filter from data after initial query. This helps to capture genomic ranges that only partially overlap with query_dat.

save_path

Where to save the processed data.

force_new

If a file already exists, download a new one anyway.

nThread

Number of threads to parallelise downloads across.

verbose

Print messages.

Examples

bigwig_metadata <- echoannot::NOTT2019_bigwig_metadata[1,]
query_dat = echodata::BST1

bw.gr <- echoannot::import_ucsc_bigwigs(query_dat = query_dat, 
                                        bigwig_metadata = bigwig_metadata)
#> Constructing GRanges query using min/max ranges across one or more chromosomes.
#> Downloading data from UCSC.
#> Importing... [1] exvivo_H3K27ac
#> Saving bigwig query ==> /tmp/Rtmp3k34Cf/file5da941675e32