Usage
## S3 method for class 'DGEList':
plotMD(object, column = 1, xlab = "Average log CPM (this sample and others)",
ylab = "log-ratio (this sample vs others)",
main = colnames(object)[column], status=object$genes$Status,
zero.weights = FALSE, prior.count = 3, ...)
## S3 method for class 'DGEGLM':
plotMD(object, column = ncol(object), coef = NULL, xlab = "Average log CPM",
ylab = "log-fold-change", main = colnames(object)[column],
status=object$genes$Status, zero.weights = FALSE, ...)
## S3 method for class 'DGELRT':
plotMD(object, xlab = "Average log CPM",
ylab = "log-fold-change", main = object$comparison,
status=object$genes$Status, \dots)
Arguments
object
an object of class DGEList
, DGEGLM
, DGEGLM
or DGEExact
.
column
integer, column of object
to be plotted.
coef
alternative to column
for fitted model objects. If specified, then column
is ignored.
xlab
character string, label for x-axis
ylab
character string, label for y-axis
main
character string, title for plot
status
vector giving the control status of each spot on the array, of same length as the number of rows of object
.
If NULL
, then all points are plotted in the default color, symbol and size.
zero.weights
logical, should spots with zero or negative weights be plotted?
prior.count
the average prior count to be added to each observation. Larger values produce more shrinkage.