Retrieve the matrix of feature weights from a SIAMCAT object

Function to extract the feature weights from a SIAMCAT object

feature_weights(siamcat, verbose=1)

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

Arguments

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 0 (no output) or 1 (print message)

Value

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

Details

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)

Examples

data(siamcat_example)
temp <- feature_weights(siamcat_example)
head(temp)
#>                                          mean.weight median.weight sd.weight
#> unclassified Fusobacterium [c:1482]       -95.094987     0.5269887 257.30611
#> unclassified Fusobacterium [c:1481]        19.793839    29.2345090  32.48733
#> Pseudoflavonifractor capillosus [h:1579]  -21.451579    30.7454712 166.60164
#> Porphyromonas asaccharolytica [h:1056]     29.182380    28.4305549  41.46582
#> Prevotella nigrescens [h:1069]             36.933694    36.2547827  40.99035
#> Peptostreptococcus stomatis [h:1530]       -5.094556    21.3835589  80.62460
#>                                          mean.rel.weight median.rel.weight
#> unclassified Fusobacterium [c:1482]        -0.0301846342      0.0004570326
#> unclassified Fusobacterium [c:1481]        -0.0001278288      0.0195451964
#> Pseudoflavonifractor capillosus [h:1579]    0.0151405614      0.0252825304
#> Porphyromonas asaccharolytica [h:1056]      0.0063587682      0.0175983706
#> Prevotella nigrescens [h:1069]              0.0235607690      0.0338731179
#> Peptostreptococcus stomatis [h:1530]       -0.0027804450      0.0207560497
#>                                          sd.rel.weight percentage
#> unclassified Fusobacterium [c:1482]         0.04926960          1
#> unclassified Fusobacterium [c:1481]         0.04043017          1
#> Pseudoflavonifractor capillosus [h:1579]    0.03123462          1
#> Porphyromonas asaccharolytica [h:1056]      0.02792042          1
#> Prevotella nigrescens [h:1069]              0.02256343          1
#> Peptostreptococcus stomatis [h:1530]        0.04215574          1