confints {ER}  R Documentation 
Confidence Intervals of Effect Differences
confints(X1, X2, confidence = 0.95, df.used = 0)
## S3 method for class 'confints'
plot(
x,
y,
xlab = "",
ylab = "normalised log2",
sorted = TRUE,
labels = FALSE,
nonZero = FALSE,
xlim = NULL,
ylim = NULL,
text.pt = 12,
...
)
X1 

X2 

confidence 
Level of confidence, default = 0.95. 
df.used 
Optional argument indicating how many degrees of freedom have been consumed during deflation. Default = 0. 
x 
Object of class 
y 
Not used. 
xlab 
X label ( 
ylab 
Y label ( 
sorted 
Logical indicating if intervals should be sorted according to their mean values, or a vector of indices/labels to sort by. 
labels 
Logical indicating if sample labels should be used on x axis. 
nonZero 
Logical indicating if intervals are required not to include zero. 
xlim 
Limits of the horizontal scale. 
ylim 
Limits of the vertical scale. 
text.pt 
Size scaling of text in the plot (default = 16). 
... 
Further arguments to 
An object of class confints
, which holds
the information needed to perform statistics or plot the
confidence intervals is returned from confints
.
The plotting routine returns a ggplot structure for plotting.
data(MS)
# Compare MS and nonMS patients within cluster 1
conf < with(MS, confints(proteins[MS == "yes" & cluster == 1,],
proteins[MS == "no" & cluster == 1,]))
p1 < plot(conf)
p2 < plot(conf, nonZero = TRUE) # Only intervals without 0.
grid.arrange(p1,p2)
# Shorter plot with labels
confShort < conf[1:10,]
p1 < plot(confShort, labels = TRUE)
p2 < plot(confShort, labels = TRUE, nonZero = TRUE)
grid.arrange(p1,p2)