Create GWAS locus zoom track

This function will plot the p-values associated with variants in a given region of the genome (genome position: x-axis; -log10(p): y-axis).

Usage

GWASTrack(
  gwas,
  region,
  ld.file = NULL,
  ld.lead.snp = NULL,
  credset.file = NULL,
  credset.threshold = 0.01,
  p.threshold = 5e-08,
  ymax = NULL,
  point.size = 1,
  point.color = "steelblue",
  show.axis = TRUE
)

Arguments

gwas

Path to GWAS summary statistics file, or a dataframe containing the gwas data in the GWAS-SSF format

region

Genomic region (GenomicRanges::GRanges or a string that can be converted to GRanges like "chr10:112900000-113100000")

ld.file

Path to LD file. Optional.

ld.lead.snp

Lead SNP for LD (required if ld.file provided)

credset.file

Path to credible set file. Optional.

credset.threshold

PIP threshold for credible sets (default: 0.01)

p.threshold

Genome-wide significance threshold (default: 5e-8)

ymax

Maximum y-axis value (default: auto)

point.size

Point size (default: 1)

point.color

Point color when no LD (default: "steelblue")

show.axis

Show x-axis (default: TRUE)

Value

ggplot2 object

Details

If an LD file is provided using the ld.file parameter, or a column named r2 is present in the input GWAS data, the variants will be colored according to their LD value.

If a fine mapping file is provided using the credset.file parameter, or a column named in_credset is present in the input GWAS data, variants in the credible set will be denoted by shape. If LD information is not provided, credible variants will also be denoted by color.