volcanor {manhattanly} | R Documentation |
Creates a volcano object
Description
An object of class volcano includes all the needed information for producing
a volcano plot of p-values against effect sizes or fold-changes. The goal is
to seperate the pre-processing of the volcano plot elements from the
graphical rendaring of the object, which could be done using any graphical
device including plot_ly
and
plot
in base R
.
Usage
volcanor(
x,
p = "P",
effect_size = "EFFECTSIZE",
snp,
gene,
annotation1,
annotation2,
...
)
Arguments
x |
A
|
p |
A chracter string denoting the column name for the p-values. Default
is |
effect_size |
A string denoting the column name for the effect size.
Default is |
snp |
A string denoting the column name for the SNP names (e.g. rs
number). This argument is optional but required if you want to highlight
any points. More generally, this column could be anything that identifies
each point being plotted. For example, in an Epigenomewide association
study (EWAS) this could be the probe name or cg number. This column should
contain |
gene |
A string denoting the column name for the GENE names. This column
could be a |
annotation1 |
A string denoting the column name for an annotation. This
column could be a |
annotation2 |
A string denoting the column name for an annotation. This
column could be a |
... |
currently ignored |
Value
An list object of class volcanor
with the following elements
- data
processed data to be used for plotting the volcano plot including the observed and expected p-values on the -log10 scale
- pName, snpName, geneName, annotation1Name, annotation2Name
The names of the columns corresponding to the data provided. This information is used for annotating the plot in the
volcanoly
function
Note
This function will return an error if any of the p-values are NA, less than 0 or greater than 1
See Also
Examples
library(manhattanly)
volcanorObj <- volcanor(HapMap)
class(volcanorObj)
head(volcanorObj)