Description Slots Author(s) References See Also Examples
ORdensity is a package for the automated discovery of differentially expressed genes. It makes use of the ORdensity method and the associated FP and dFP values to detect the most likely true positives.
Object of class ORdensity includes all potential diffentially expressed genes given miroarray data measured in two experimental conditions.
positive
Matrix including microarray data measured under experimental condition 1.
negative
matrix including microarray data measured under experimental condition 2.
labels
Vector of characters identifying the genes, by default
rownames(positive) is inherited. If NULL,
the genes are named ‘Gene1’, ..., ‘Genen' according to the order given in positive
.
B
Numeric value indicating the number of bootstrap iteration. By default, B
=100.
scale
Logical value to indicate whether the scaling of the difference of quatiles should be done.
alpha
Numeric value to control the bootstrap threshold. By default 0.05.
fold
Numeric value, by default fold
=10. It controls the number of partitions.
probs
Vector of numerics. It sets the quantiles to be considered. By default
probs = c(0.25, 0.5, 0.75)
.
weights
Vector of numerics. It controls the weights given to the quantiles set in probs
.
By default weights = c(1/4, 1/2, 1/4)
.
K
Numeric value to set the number of nearest neighbours. By default K=10
.
out
List containing the potential DE genes and their characteristics. ...
Jose Maria Martinez Otzeta josemaria.martinezo@ehu.eus
Jose Maria Martinez-Otzeta, Itziar Irigoien, Concepcion Arenas
Irigoien and Arenas (2018) Identification of differentially expressed genes by means of outlier detection. BMC Bioinformatics, 19:317
summary.ORdensity
, preclusteredData
,
plot.ORdensity
, silhouetteAnalysis
,
clusplotk
, compute.ORdensity
,
findbestK
, findDEgenes
, ORdensity
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