import_ucsc_bigwigs: Import bigwig files from the UCSC Genome Browser

In RajLabMSSM/echoannot: echoverse module: Annotate fine-mapping results

Import bigwig files from the UCSC Genome Browser

Description

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

Usage

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)

RajLabMSSM/echoannot documentation built on Oct. 26, 2023, 2:41 p.m.