Get widow limits

Source: R/get_window_limits.R

Get genomic window size limits for a locus plot.

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)
#> + Inferring genomic limits for window: 50000
xlims <- get_window_limits(dat = dat, zoom = "all")
#> + Inferring genomic limits for window: all
xlims <- get_window_limits(dat = dat, zoom = "5x")
#> + Inferring genomic limits for window: 5x