manhattan_plot_bGWAS: Manhattan Plot from bGWAS results
In n-mounier/bGWAS: Bayesian Genome-Wide Association Study

manhattan_plot_bGWAS

R Documentation

Manhattan Plot from bGWAS results

Description

Creates a Manhattan Plot from bGWAS results (for performance, only SNPs with p-value or FDR < 0.05 are plotted)

Usage

manhattan_plot_bGWAS(
  obj,
  save_file = F,
  file_name = NULL,
  annotate = T,
  SNPs = NULL,
  results = "BF"
)

Arguments

`obj`	an object of class bGWAS created using `bGWAS()`
`save_file`	A logical indicating if the graphic should be saved, `default=FALSE`, graphic will be displayed on the on-screen device
`file_name`	The name of the file saved (is `save_file` is `TRUE`) `default=NULL`, will used NameOfYourAnalysis_ManhattanPlot.png
`annotate`	A logical indicating if the significant SNPs identified in the analysis should be annotated on the plot, `default=TRUE` If your results are not pruned or if you have a high number of significant SNPs, be aware that `annotate=TRUE` might decrease readability of the figure. You could define a set of SNPs to annotate using `SNPs`.
`SNPs`	A data.frame containing the SNPs (rsid) to annotate in the first column, and optionnally the text that should be plotted in the second column, and the color in the third column, `default=NULL`, only evaluated if `annotate=TRUE`.
`results,`	"BF" / "posterior" / "direct", `default="BF"`

Details

If results = "BF", BF p-values / fdr-values will be used.
If results = "direct", direct effect p-values / fdr-values will be used.
If results = "posterior", posterior effect p-values / fdr-values will be used.