Objects from the class
New objects can be created using calls of the form
new("SetMethodsSims", null.dist, perc.samples, spiked.set.sizes,
GeneSizes, GeneSets, Coverage, EventsBySample, Mutations, Scores,
results) Slots
null.dist:- Object of class
"character".
Can be either "Passenger null" or
"Permutation null," depending on what
method is used to get the null data. perc.samples:- Object of class
"numeric".
Vector representing the probabilities
of the spiked-in gene-sets being
altered in any given sample, as percentages;
for example
perc.samples = c(75, 90)
means that these probabilities are
0.75 and 0.90. spiked.set.sizes:- Object of class
"numeric".
Vector representing the sizes, in genes,
of the spiked-in gene-sets;
for example, if
perc.samples = c(75, 90) and
spiked.set.sizes = c(50, 100),
there would be 4 spiked-in sets,
one with 50 genes and probability of
being altered of 0.75 in each sample,
one with 50 genes and probability of
being altered of 0.90 in each sample,
one with 100 genes and probability of
being altered of 0.75 in each sample, and
one with 100 genes and probability of
being altered of 0.90 in each sample. GeneSets:- Object of class
"list".
The entries of the list correspond to
gene-sets and give the genes annotated to
them. cma.alter:- Object of class
"list".
The entries of the list are objects similar to
the GeneAlter objects and correspond to the
simulation iterations. cma.cov:- Object of class
"list".
The entries of the list are objects similar to
the GeneCov objects and correspond to the
simulation iterations. cma.samp:- Object of class
"list".
The entries of the list are objects similar to
the GeneSamp objects and correspond to the
simulation iterations. Scores:- Object of class
"list".
The entries of this list are the output of
cma.scores and correspond to the
simulation iterations. results:- Object of class
"list".
The entries of this list are the output of
cma.set.stat and correspond to the
simulation iterations.
Methods
- show
signature(object = "SetMethodsSims")