This function computes the entropy of a counts matrix from a MoleculeExperiment object based on the given assay type.
Arguments
- me
A MoleculeExperiment object.
- featureTypes
A character string specifying the feature type. Supported values include "subsector", "subconcentric", "supersector", and "superconcentric".
- nCores
Number of cores
- ...
arguments passing to
CountsMatrix
Examples
data(example_me)
me <- loadBoundaries(me)
ent <- EntropyMatrix(me, c("subsector", "subconcentric",
"supersector", "superconcentric"), nCores = 1)
lapply(ent, head, n = 4)
#> $subsector
#> sample1.67500 sample1.67512 sample1.67515 sample1.67521
#> 2010300C02Rik 0.5623351 0.6931472 0.6365142 0.6931472
#> Acsbg1 0.6931472 0.6931472 0.6931472 0.0000000
#> Adamts2 0.0000000 0.0000000 0.0000000 0.0000000
#> Adamtsl1 0.0000000 0.0000000 0.0000000 0.0000000
#> sample1.67527 sample2.65043 sample2.65044 sample2.65051
#> 2010300C02Rik 0 0 0 0.0000000
#> Acsbg1 0 0 0 0.6931472
#> Adamts2 0 0 0 0.0000000
#> Adamtsl1 0 0 0 0.0000000
#> sample2.65055 sample2.65063 sample2.65064 sample2.65067
#> 2010300C02Rik 1.5498260 0 0.6931472 0
#> Acsbg1 0.6931472 0 0.0000000 0
#> Adamts2 0.0000000 0 0.0000000 0
#> Adamtsl1 0.0000000 0 0.0000000 0
#> sample2.65070 sample2.65071
#> 2010300C02Rik 0 0.0000000
#> Acsbg1 0 0.6931472
#> Adamts2 0 0.0000000
#> Adamtsl1 0 0.0000000
#>
#> $subconcentric
#> sample1.67500 sample1.67512 sample1.67515 sample1.67521
#> 2010300C02Rik 0.5623351 0.6931472 0.6365142 0
#> Acsbg1 0.6931472 0.0000000 0.6931472 0
#> Adamts2 0.0000000 0.0000000 0.0000000 0
#> Adamtsl1 0.0000000 0.0000000 0.0000000 0
#> sample1.67527 sample2.65043 sample2.65044 sample2.65051
#> 2010300C02Rik 0 0 0 0
#> Acsbg1 0 0 0 0
#> Adamts2 0 0 0 0
#> Adamtsl1 0 0 0 0
#> sample2.65055 sample2.65063 sample2.65064 sample2.65067
#> 2010300C02Rik 1.2770343 0 0.6931472 0
#> Acsbg1 0.6931472 0 0.0000000 0
#> Adamts2 0.0000000 0 0.0000000 0
#> Adamtsl1 0.0000000 0 0.0000000 0
#> sample2.65070 sample2.65071
#> 2010300C02Rik 0 0
#> Acsbg1 0 0
#> Adamts2 0 0
#> Adamtsl1 0 0
#>
#> $supersector
#> sample1.67500 sample1.67512 sample1.67515 sample1.67521
#> 2010300C02Rik 0 1.332179 0.6931472 0.6931472
#> Acsbg1 0 0.000000 0.6931472 0.6931472
#> Adamts2 0 0.000000 0.0000000 0.0000000
#> Adamtsl1 0 0.000000 0.0000000 0.0000000
#> sample1.67527 sample2.65043 sample2.65044 sample2.65051
#> 2010300C02Rik 0 0.5623351 1.039721 0.5982696
#> Acsbg1 0 0.0000000 0.000000 0.9502705
#> Adamts2 0 0.0000000 0.000000 0.0000000
#> Adamtsl1 0 0.0000000 0.000000 0.0000000
#> sample2.65055 sample2.65063 sample2.65064 sample2.65067
#> 2010300C02Rik 0.000000 0.6931472 0 0.0000000
#> Acsbg1 1.559581 1.0114043 0 0.6931472
#> Adamts2 0.000000 0.0000000 0 0.0000000
#> Adamtsl1 0.000000 0.0000000 0 0.0000000
#> sample2.65070 sample2.65071
#> 2010300C02Rik 0.0000000 0.0000000
#> Acsbg1 0.5623351 0.6365142
#> Adamts2 0.0000000 0.0000000
#> Adamtsl1 0.0000000 0.0000000
#>
#> $superconcentric
#> sample1.67500 sample1.67512 sample1.67515 sample1.67521
#> 2010300C02Rik 1.5607104 1.05492 0.6931472 0.0000000
#> Acsbg1 0.6931472 0.00000 0.6931472 0.6931472
#> Adamts2 0.0000000 0.00000 0.0000000 0.0000000
#> Adamtsl1 0.0000000 0.00000 0.0000000 0.0000000
#> sample1.67527 sample2.65043 sample2.65044 sample2.65051
#> 2010300C02Rik 0.0000000 1.039721 1.386294 1.549826
#> Acsbg1 0.6931472 0.000000 0.000000 1.054920
#> Adamts2 0.0000000 0.000000 0.000000 0.000000
#> Adamtsl1 0.0000000 0.000000 0.000000 0.000000
#> sample2.65055 sample2.65063 sample2.65064 sample2.65067
#> 2010300C02Rik 0.6931472 0.6931472 1.386294 0.0000000
#> Acsbg1 1.3208883 1.3296613 0.000000 0.6931472
#> Adamts2 0.0000000 0.0000000 0.000000 0.0000000
#> Adamtsl1 0.0000000 0.0000000 0.000000 0.0000000
#> sample2.65070 sample2.65071
#> 2010300C02Rik 0.6931472 0.0000000
#> Acsbg1 0.6931472 0.6365142
#> Adamts2 0.0000000 0.0000000
#> Adamtsl1 0.0000000 0.0000000
#>