deGenes2by2BootT {maigesPack} | R Documentation |
This function takes an object of class maiges
and do
differential expression analysis for the genes onto dataset, comparing
only two samples by a bootstrap of t statistics method.
deGenes2by2BootT(data=NULL, sLabelID=names(data@Slabels)[1], sTypeComp=NULL, doClust=TRUE, ...)
data |
object of class maiges . |
sLabelID |
character string giving the sample label ID to be used. |
sTypeComp |
list with character vectors specifying the two sample types to be compared. |
doClust |
logical indicating if the object generated from this analysis will be used for cluster analysis. Defaults to TRUE. |
... |
additional parameters for functions
t.test , wilcox.test or
bootstrapT . |
This function calculate t statistics and p-values by re-sampling of
the data using the function bootstrapT
.
There is the option to do the t test directly, using the function
deGenes2by2Ttest
, or to do the non-parametric Wilcox
test using the function deGenes2by2Wilcox
.
The result of this function is an object of class
maigesDE
if doClust
if FALSE or of class
maigesDEcluster
if it is TRUE.
Gustavo H. Esteves <gesteves@vision.ime.usp.br>
bootstrapT
, deGenes2by2Ttest
and deGenes2by2Wilcox
.
## Loading the dataset data(gastro) ## Doing bootstrap from t statistic test fot 'Type' sample label, k=1000 ## specifies one thousand bootstraps gastro.boot = deGenes2by2BootT(gastro.summ, sLabelID="Type", k=1000) gastro.boot