manhattanPlot: Manhattan Plot for MDT and MLGWAS objects.

In olivmrtn/MachineLearningGWAS: Machine Learning for Genome Wide Association Studies

Description

Plot a Manhattan Plots for MDT and MLGWAS objects. Can use any numeric value in annotations(x) as specified by value argument. Can also use feature importance as found in featimp(mlgwas) if value is an MLGWAS object.

Usage

manhattanPlot(x, value, group = "CHROM", pos = "POS", f = function(value)
  -log10(value), col = c("blue", "orange"))

## S4 method for signature 'MDT,ANY'
manhattanPlot(x, value, group = "CHROM", pos = "POS",
  f = function(value) -log10(value), col = c("blue", "orange"))

## S4 method for signature 'MDT,MLGWAS'
manhattanPlot(x, value, group = "CHROM", pos = "POS",
  f = function(value) -log10(value), col = c("blue", "orange"))

Arguments

x	MDT object.
value	character specifying which column of annotations(x) should be used as values. For example, call annotateStat and then use Fisher's exact test p-values. Can also be MLGWAS; plots feature importance.
group	character specifying which column of annotations(x) specifying grouping of 'x' axis such as chromosome number or MLGWAS object.
pos	character specifying which column of annotations(x) specifying position on 'x' axis.
f	Some function that modifies a vector of integers. For example, -log10 for p-values.
col	Plot colors.

Value

A ggplot Manhattan plot.

olivmrtn/MachineLearningGWAS documentation built on May 24, 2019, 12:52 p.m.