"plotMA"(object, alpha = 0.1, main = "", xlab = "mean of normalized counts", ylim, MLE = FALSE, ...)
"plotMA"(object, alpha, main = "", xlab = "mean of normalized counts", ylim, MLE = FALSE, ...)
DESeqResults
object produced by results
;
or a DESeqDataSet
processed by DESeq
, or the
individual functions nbinomWaldTest
or nbinomLRT
results
was run with addMLE=TRUE
.
Note that the MLE will be plotted regardless of this argument, if DESeq() was run
with betaPrior=FALSE
.plotMA
if object
is DESeqResults
or to results
if object is
DESeqDataSet
data.frame
and passing this to the plotMA
method
for data.frame
from the geneplotter package.
The code of this function can be seen with:
getMethod("plotMA","DESeqDataSet")
If users wish to modify the graphical parameters of the plot,
it is recommended to build the data.frame in the
same manner and call plotMA
.
dds <- makeExampleDESeqDataSet()
dds <- DESeq(dds)
plotMA(dds)
res <- results(dds)
plotMA(res)
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