get_window_limits: Get widow limits

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

Get widow limits

Description

Get genomic window size limits for a locus plot.

Usage

get_window_limits(
  dat,
  index_as_center = TRUE,
  zoom = NULL,
  genomic_units = "Mb",
  verbose = TRUE
)

Arguments

dat	Data.
index_as_center	Use the index/lead SNP (the SNP with the smallest P-value) as the center point for the window.
zoom	Zoom into the center of the locus when plotting (without editing the fine-mapping results file). You can provide either: The size of your plot window in terms of basepairs (e.g. zoom=50000 for a 50kb window). How much you want to zoom in (e.g. zoom="1x" for the full locus, zoom="2x" for 2x zoom into the center of the locus, etc.). You can pass a list of window sizes (e.g. c(50000,100000,500000)) to automatically generate multiple views of each locus. This can even be a mix of different style inputs: e.g. c("1x","4.5x",25000).
genomic_units	Which genomic units to return window limits in.
verbose	Print messages.

See Also

Other plot: name_filter_convert()

Examples

dat <- echodata::BST1
xlims <- get_window_limits(dat = dat, zoom = 50000)
xlims <- get_window_limits(dat = dat, zoom = "all")
xlims <- get_window_limits(dat = dat, zoom = "5x")

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