Description Usage Arguments Value Note See Also Examples
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
.
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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 |
An list object of class volcanor
with the following elements
processed data to be used for plotting the volcano plot including the observed and expected p-values on the -log10 scale
The names
of the columns corresponding to the data provided. This information is used
for annotating the plot in the volcanoly
function
This function will return an error if any of the p-values are NA, less than 0 or greater than 1
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