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Miami plot

Source: R/GXwasR_main_functions.R
GXWASmiami.Rd

This function generates Miami plots for GWAS and XWAS.

Usage

GXWASmiami(
  ResultDir = tempdir(),
  FemaleWAS,
  MaleWAS,
  snp_pval = 1e-08,
  Xchr = FALSE
)

Arguments

ResultDir

Character string for the folder path where the outputs will be saved.

FemaleWAS

R dataframe of summary statistics of GWAS or XWAS of female samples with four columns, SNP(Variant), CHR(Chromosome number), POS(Base pair position) and pvalue(P-value of the test). This can be generated by running FM01comb or FM02comb model with GXWAS function.

MaleWAS

R dataframe of summary statistics of GWAS or XWAS of male samples with four columns, SNP(Variant), CHR(Chromosome number), POS(Base pair position) and pvalue(P-value of the test). This can be generated by running FM01comb or FM02comb model with GXWAS function.

snp_pval

Numeric value as p-value threshold for annotation. SNPs below this p-value will be annotated on the plot. The default is 1e-08.

Xchr

Boolean value, TRUE or FALSE, specifying whether to generate Miami plot for stratified XWAS or not. The default is TRUE.

Value

Invisibly returns NULL. Generates and saves Miami plots as a side effect.

Examples

data("Ffile", package = "GXwasR")
data("Mfile", package = "GXwasR")
FemaleWAS <- na.omit(Ffile[, c("SNP", "CHR", "BP", "P")])
colnames(FemaleWAS) <- c("SNP", "CHR", "POS", "pvalue")
MaleWAS <- na.omit(Mfile[, c("SNP", "CHR", "BP", "P")])
colnames(MaleWAS) <- c("SNP", "CHR", "POS", "pvalue")

GXWASmiami(FemaleWAS = FemaleWAS, MaleWAS = MaleWAS, snp_pval = 0.05)
#> • Generating Miami plots for stratified test.
#> ℹ Saving plot to /var/folders/d6/gtwl3_017sj4pp14fbfcbqjh0000gp/T//RtmpO7c0S8/Stratified_GWAS.png

#> ✔ Miami plot of stratified GWAS is saved in /var/folders/d6/gtwl3_017sj4pp14fbfcbqjh0000gp/T//RtmpO7c0S8