kmeansDesign {recoup} | R Documentation |
This function performs k-means clustering on
recoup
generated profile matrices and
stores the result as a factor in the design element.
If no design is present, then one is created from the
k-means result.
kmeansDesign(input, design = NULL, kmParams)
input |
a list object created from
|
design |
See the respective argument in
|
kmParams |
Contains parameters for k-means
clustering on profiles. See the respective argument
in |
The design data frame, either created from scratch or augmented by k-means clustering.
Panagiotis Moulos
# Load some data data("recoup_test_data",package="recoup") # Calculate coverages test.tss <- recoup( test.input, design=NULL, region="tss", type="chipseq", genome=test.genome, flank=c(1000,1000), selector=NULL, plotParams=list(plot=FALSE,profile=TRUE, heatmap=TRUE,device="x11"), rc=0.1 ) # Re-design based on k-means kmParams=list(k=2,nstart=20,algorithm="MacQueen",iterMax=20, reference=NULL) design <- kmeansDesign(test.tss$data,kmParams=kmParams)