`feature_weights-methods.Rd`

Function to extract the feature weights from a SIAMCAT object

```
feature_weights(siamcat, verbose=1)
# S4 method for siamcat
feature_weights(siamcat, verbose = 1)
```

siamcat | (Required). A siamcat-class object that contains trained models |
---|---|

verbose | integer, if the slot is empty, should a message be printed?
values can be either |

A dataframe containing mean/median feature weight and
additional info or `NULL`

The function extracts the weight matrix from all trained models (see weight_matrix) and computes several metrics on the feature weights:

`mean.weight`

- mean weight across trained models`median.weight`

- median weight across trained models`sd.weight`

- standard deviation of the weight across trained models`mean.rel.weight`

- mean**relative**weight across trained models (each model is normalized by the absolute of all weights)`median.rel.weight`

- median**relative**weight across trained models`sd.rel.weight`

- standard deviation of the**relative**weight across trained models`percentage`

- percentage of models in which this feature was selected (i.e. non-zero)

```
data(siamcat_example)
temp <- feature_weights(siamcat_example)
head(temp)
#> mean.weight median.weight sd.weight
#> unclassified Fusobacterium [c:1482] -22.911573 -8.840574 33.90188
#> unclassified Fusobacterium [c:1481] 6.531374 4.258957 26.13803
#> Pseudoflavonifractor capillosus [h:1579] 26.610582 27.392341 21.85843
#> Porphyromonas asaccharolytica [h:1056] 13.051833 11.900938 14.93073
#> Prevotella nigrescens [h:1069] 28.578953 23.931092 30.93435
#> Peptostreptococcus stomatis [h:1530] 7.996267 1.586044 22.85606
#> mean.rel.weight median.rel.weight
#> unclassified Fusobacterium [c:1482] -0.041840339 -0.014960815
#> unclassified Fusobacterium [c:1481] -0.008315680 0.003723249
#> Pseudoflavonifractor capillosus [h:1579] 0.023496680 0.028361676
#> Porphyromonas asaccharolytica [h:1056] 0.008233728 0.015489473
#> Prevotella nigrescens [h:1069] 0.032268581 0.036707175
#> Peptostreptococcus stomatis [h:1530] -0.002017143 0.002353617
#> sd.rel.weight percentage
#> unclassified Fusobacterium [c:1482] 0.05649630 0.9
#> unclassified Fusobacterium [c:1481] 0.03492352 1.0
#> Pseudoflavonifractor capillosus [h:1579] 0.02528359 1.0
#> Porphyromonas asaccharolytica [h:1056] 0.01349503 1.0
#> Prevotella nigrescens [h:1069] 0.02671583 1.0
#> Peptostreptococcus stomatis [h:1530] 0.02660175 1.0
```