Function to retrieve the results of association testing

associations(siamcat, verbose=1)

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

Arguments

siamcat

(Required). An instance of siamcat-class containing the results of association testing

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 data.frame of association testing results or NULL

Details

The function returns the results of the association testing procedure as dataframe. See check.associations for more details.

Examples

data(siamcat_example)
temp <- associations(siamcat_example)
head(temp)
#>                                                 fc        p.val       auc
#> unclassified Fusobacterium [c:1482]      0.6455199 9.835836e-11 0.7497856
#> unclassified Fusobacterium [c:1481]      0.8870737 2.999095e-08 0.7310249
#> Pseudoflavonifractor capillosus [h:1579] 0.3248662 1.454894e-05 0.7184820
#> Porphyromonas asaccharolytica [h:1056]   0.4285522 1.914120e-05 0.6410806
#> Prevotella nigrescens [h:1069]           0.2672896 5.114510e-05 0.5988422
#> Peptostreptococcus stomatis [h:1530]     0.8778735 1.132256e-04 0.6861063
#>                                           auc.ci.l  auc.ci.h   pr.shift
#> unclassified Fusobacterium [c:1482]      0.6760295 0.8235417 0.44875643
#> unclassified Fusobacterium [c:1481]      0.6512266 0.8108232 0.39558319
#> Pseudoflavonifractor capillosus [h:1579] 0.6319394 0.8050246 0.03409091
#> Porphyromonas asaccharolytica [h:1056]   0.5708510 0.7113102 0.27144082
#> Prevotella nigrescens [h:1069]           0.5424919 0.6551925 0.19618353
#> Peptostreptococcus stomatis [h:1530]     0.5904339 0.7817787 0.16037736
#>                                                pr.n      pr.p      bcol
#> unclassified Fusobacterium [c:1482]      0.07954545 0.5283019 #A5002685
#> unclassified Fusobacterium [c:1481]      0.17045455 0.5660377 #A5002685
#> Pseudoflavonifractor capillosus [h:1579] 0.96590909 1.0000000 #A5002685
#> Porphyromonas asaccharolytica [h:1056]   0.06818182 0.3396226 #A5002685
#> Prevotella nigrescens [h:1069]           0.01136364 0.2075472 #A5002685
#> Peptostreptococcus stomatis [h:1530]     0.50000000 0.6603774 #A5002685
#>                                                 p.adj
#> unclassified Fusobacterium [c:1482]      2.754034e-09
#> unclassified Fusobacterium [c:1481]      4.198733e-07
#> Pseudoflavonifractor capillosus [h:1579] 1.339884e-04
#> Porphyromonas asaccharolytica [h:1056]   1.339884e-04
#> Prevotella nigrescens [h:1069]           2.864126e-04
#> Peptostreptococcus stomatis [h:1530]     5.283861e-04