Print on screen a simple description of the content of objects of class phylterfinal.
Usage
# S3 method for class 'phylterfinal'
print(x, ...)Examples
data(carnivora)
res <- phylter(carnivora, parallel = FALSE)
#>
#> Number of Genes: 125
#> Number of Species: 53
#> --------
#> Initial score: 0.86235
#> 28 new cells to remove -> New score: 0.90272 -> OK
#> 18 new cells to remove -> New score: 0.90833 -> OK
#> 16 new cells to remove -> New score: 0.91501 -> OK
#> 18 new cells to remove -> New score: 0.92561 -> OK
#> 5 new cells to remove -> New score: 0.93404 -> OK
#> 4 new cells to remove -> New score: 0.93692 -> OK
#> 2 new cells to remove -> New score: 0.93712 -> OK
#> 1 new cells to remove -> New score: 0.94392 -> OK
#> 1 new cells to remove -> New score: 0.94417 -> OK
#> 1 new cells to remove -> New score: 0.94426 -> OK
#> => No more outliers detected -> Checking for complete gene outliers
#> => No more outliers detected -> STOPPING OPTIMIZATION
#> --------
#>
#> Total number of outliers detected: 94
#> Number of complete gene outliers : 0
#> Number of complete species outliers : 0
#>
#> Gain (concordance between matrices): 8.19%
#> Loss (data filtering): 1.42%
print(res$Final)
#> Phylter Analysis - final state
#> List of class phylterfinal
#>
#> Object Dimension
#> 1 $WR 53 x 125
#> 2 $RV 125 x 125
#> 3 $weights 125
#> 4 $compromise 53 x 53
#> 5 $F 53 x 8
#> 6 $PartialF 125
#> 7 $species.order 53
#> 8 $AllOptiScores 11
#> 9 $CELLSREMOVED 94 x 2
#> 10 $Outliers 94 x 2
#> 11 $CompleteOutliers 2
#> 12 $matrices 125
#> Content
#> 1 Species x Genes reference matrix
#> 2 Genes x Genes RV correlation coefficients matrix
#> 3 Weight of each gene in the compromise
#> 4 Species x Species compromise matrix
#> 5 Distatis coordinates of compromise
#> 6 Distatis coordinates of gene matrices (list)
#> 7 Name and order of species
#> 8 Evolution of quality of compromise (11 steps)
#> 9 Index of cells removed (may contain imputed cells)
#> 10 Outliers detected (one row = one outlier cell)
#> 11 Complete outliers (Gene and Species, if any)
#> 12 Species x Species gene matrices (list)