ROADMAP_plot: Plot annotation peaks: ROADMAP

In RajLabMSSM/echoplot: echoverse module: Locus plot creation for fine-mapping and colocalization studies

Plot annotation peaks: ROADMAP

Description

Import annotation from ROADMAP, filter to only those within the range of dat, and then plot the peaks. If the annotation has already been downloaded previously, it will be reused.

Usage

ROADMAP_plot(
  dat,
  roadmap_query,
  lib_name = "Roadmap.ChromatinMarks_CellTypes",
  locus_dir = tempdir(),
  limit_files = NULL,
  n_top = 5,
  adjust = 0.2,
  force_new = FALSE,
  show_plot = FALSE,
  conda_env = "echoR_mini",
  nThread = 1,
  verbose = TRUE
)

Arguments

dat	data.table with at least the following columns: SNP SNP RSID CHR chromosome POS position
roadmap_query	Search all columns in the Roadmap annotations metadata and only query annotations that contain your keywords. Can provide multiple keywords in list form: c("placenta","liver","monocytes")
lib_name	Name of the data library to use.
locus_dir	Locus-specific directory.
limit_files	Limit the number of annotation files queried (for faster testing).
n_top	Number of top annotations to be plotted (passed to ROADMAP_query).
adjust	The granularity of the peaks.
force_new	Download and prepare a new query even if the file already exists locally (Default: FALSE).
show_plot	Print the plot.
conda_env	Conda environment to search for tabix in.
nThread	Number of threads to parallelise downloading annotations over.
verbose	Print messages.

Value

A named list containing:

• "data"GRanges object within the queried coordinates.

• "plot"ggbio plot.

Examples

dat <- echodata::BST1[seq_len(1000),]
roadmap_out <- echoplot::ROADMAP_plot(
    dat = dat,
    roadmap_query = "monocyte")

RajLabMSSM/echoplot documentation built on Oct. 24, 2023, 2:41 a.m.