plotManhattanQC: Create a QC Manhattan plots from rTASSEL association output
In maize-genetics/rTASSEL: R Front-End for TASSEL

plotManhattanQC

R Documentation

Create a QC Manhattan plots from rTASSEL association output

Description

This function allows for quick generation of a QC plot from rTASSEL association statistical output data. The main goal of this function is to provide "zoomed" in Manhattan plots that typically fall within genomic ranges of interest plus a flanking window up- and downstream of the ranges.

Usage

plotManhattanQC(
  assocRes,
  trait = NULL,
  gr,
  window = 1e+05,
  threshold = NULL,
  classicNames = FALSE,
  interactive = FALSE,
  verbose = TRUE
)

Arguments

`assocRes`	An object of type `AssociationResults`
`trait`	Which phenotypic trait do you want to plot? If set to `NULL`, this will generate a faceted plot with all mapped traits.
`gr`	Genomic ranges of interest. Can be passed as a `GRanges` object or a `data.frame` object.
`window`	Window size (base-pairs) flanking surround reference range. Defaults to `100000` (100,000 base-pairs).
`threshold`	User-defined `-log_{10}(p)`-value threshold for significant marker determination. Once specified any marker points higher than this line will be highlighted.
`classicNames`	Do you want to plot classical gene names instead? NOTE: this will need a `classical_id` column for the "ranges of interest" data. Defaults to `FALSE`.
`interactive`	Do you want to produce an interactive visualization? Defaults to `FALSE`.
`verbose`	Should messages be printed to console? Defaults to `FALSE`.