region: Regional plot

In kenhanscombe/associatr: Genetic Association Plots

Description

Plots is a negative log base 10 p-value against genomic position scatterplot for a relatively small genomic "window". Below this Association layer, there are additional layers or "tracks" providing biological context: hg19 build 37 combined Recombination Rate, known refSeq Genes, and optional tracks including genetic regulation information.

Usage

region(
  data,
  recomb_map,
  target,
  chromosome,
  target_bp,
  pop = "EUR",
  window_kb = 150,
  regulation = FALSE,
  token = NULL
)

Arguments

data	A genetic association results dataframe.
recomb_map	A recombination map dataframe with header and obligatory columns 'position' (genomic position), 'combined_rate' (combined recombination rate cM/Mb), and 'chr' (chromosome). Use get_map to retrieve a build 37 map for any 1000 genomes phase 3 population.
target	A character vector for the variant of interest.
chromosome	An integer indicating the chromosome on which the region sits.
target_bp	A integer indicating base pair position in the centre of the region.
pop	A string argument passed to LDlinkR. A 1000 Genomes population codes, or super population codes can be used. Multiple codes allowed. Default is super population "EUR" (includes "CEU", "TSI", "FIN", "GBR", "IBS").
window_kb	A integer indicating window size in kb (default is 150kb), to be included either side of the target_bp location. Maximum is 500kb.
regulation	A boolean (default FALSE) indicating whether or not to include regulation tracks.
token	An LDlinkR 'Personal Access Token'. Default is 'NULL'. See Details.

Details

You will need a genetic map. Use get_map to download 1000 Genomes phase 3 recombination map data. To retrieve LD data for the region of interest, you will need an LDlinkR 'Personal Access Token' described here. Apply for a token here.

kenhanscombe/associatr documentation built on Nov. 13, 2020, 9:24 a.m.