Random Forest Prediction Based Score

Arguments

x: A phyloseq object
group_col: A column in phyloseq::sample_data with all control and case labels.
case_label: A character string specifying case/disease labels in group_col.
seed_value: The random seed of your session for reproducibility.
add_tuneRF_params: A list of arguments to pass for randomForest::tuneRF
ntree: Number of trees. See randomForest::randomForest
plot_roc: Logical TRUE or FALSE to plot ROC curve.
...: Additional arguments if necessary for randomForest::randomForest.

Value

A data frame with oob.score score and sample information

Details

An out-of-bag probability of Random Forest of being classified as case or diseased group.

The original article Saffouri GB, Shields-Cutler R et al. 2019 reported a Symptom Index abbreviated as SI. In this approach the feature abundances are used for Random Forest classification and the resulting out of bag (OOB) predicted probability of being classified in disease group is considered as an SI or also dysbiosis index. The dysbiosisOBB function in this package allows for calculating this measure with some level of freedom of 'tuneRF' and 'randomForest' parameters via the randomForest R package.

References

Saffouri GB, Shields-Cutler R et al. (2019). Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders. Nature communications, 10(1), pp.1-11.

Author

Sudarshan A. Shetty

Examples

data("WirbelJ_2018")
# data are relative abundances summed to 100 or
# near 100 val
dysbiosis.oob <- dysbiosisOBB(WirbelJ_2018,
                              group_col = "disease",
                              case_label = "CRC",
                              seed_value = 1235,
                              add_tuneRF_params = list(ntreeTry=100,
                                                       stepFactor=1.5,
                                                       improve=0.01,
                                                       trace=TRUE,
                                                       dobest=FALSE),
                              ntree = 100, # increase for real data
                              plot_roc = TRUE)
#> The random seed of your session for reproducibility is: 1235
#> mtry = 23  OOB error = 20.8% 
#> Searching left ...
#> mtry = 16 	OOB error = 22.4% 
#> -0.07692308 0.01 
#> Searching right ...
#> mtry = 34 	OOB error = 19.2% 
#> 0.07692308 0.01 
#> mtry = 51 	OOB error = 17.6% 
#> 0.08333333 0.01 
#> mtry = 76 	OOB error = 18.4% 
#> -0.04545455 0.01 
#> The mtry used is : 51
#> Setting levels: control = CRC, case = healthy
#> Setting direction: controls > cases


head(dysbiosis.oob)
#>                     oob.score   study_name          subject_id body_site
#> CCMD11006829ST-21-0 0.9459459 WirbelJ_2018 CCMD11006829ST-21-0     stool
#> CCMD12232071ST-21-0 0.7714286 WirbelJ_2018 CCMD12232071ST-21-0     stool
#> CCMD13071240ST-21-0 0.6969697 WirbelJ_2018 CCMD13071240ST-21-0     stool
#> CCMD13934959ST-21-0 0.7714286 WirbelJ_2018 CCMD13934959ST-21-0     stool
#> CCMD14479708ST-21-0 0.6578947 WirbelJ_2018 CCMD14479708ST-21-0     stool
#> CCMD18872694ST-21-0 0.8787879 WirbelJ_2018 CCMD18872694ST-21-0     stool
#>                     study_condition disease age age_category gender country
#> CCMD11006829ST-21-0             CRC     CRC  42        adult female     DEU
#> CCMD12232071ST-21-0             CRC     CRC  75       senior   male     DEU
#> CCMD13071240ST-21-0             CRC     CRC  66       senior female     DEU
#> CCMD13934959ST-21-0             CRC     CRC  56        adult   male     DEU
#> CCMD14479708ST-21-0             CRC     CRC  74       senior   male     DEU
#> CCMD18872694ST-21-0             CRC     CRC  63        adult   male     DEU
#>                     non_westernized sequencing_platform DNA_extraction_kit
#> CCMD11006829ST-21-0              no       IlluminaHiSeq              Gnome
#> CCMD12232071ST-21-0              no       IlluminaHiSeq              Gnome
#> CCMD13071240ST-21-0              no       IlluminaHiSeq              Gnome
#> CCMD13934959ST-21-0              no       IlluminaHiSeq              Gnome
#> CCMD14479708ST-21-0              no       IlluminaHiSeq              Gnome
#> CCMD18872694ST-21-0              no       IlluminaHiSeq              Gnome
#>                         PMID number_reads number_bases minimum_read_length
#> CCMD11006829ST-21-0 30936547     83456496   7310970279                  45
#> CCMD12232071ST-21-0 30936547     65269931   5370021950                   2
#> CCMD13071240ST-21-0 30936547     63427722   5486983593                  45
#> CCMD13934959ST-21-0 30936547     36979669   3186342244                  45
#> CCMD14479708ST-21-0 30936547     65475493   5637718108                  45
#> CCMD18872694ST-21-0 30936547     55300211   4780095276                  45
#>                     median_read_length NCBI_accession      curator BMI    tnm
#> CCMD11006829ST-21-0                 94           <NA> Paolo_Manghi  35 t3n0m0
#> CCMD12232071ST-21-0                 88           <NA> Paolo_Manghi  28 t3n2m0
#> CCMD13071240ST-21-0                 93           <NA> Paolo_Manghi  23 t3n0m0
#> CCMD13934959ST-21-0                 93           <NA> Paolo_Manghi  27 t3n0m0
#> CCMD14479708ST-21-0                 92           <NA> Paolo_Manghi  26 t3n0m1
#> CCMD18872694ST-21-0                 93           <NA> Paolo_Manghi  25 t3n1m0
#>                     ajcc nspecies group
#> CCMD11006829ST-21-0   ii      144  case
#> CCMD12232071ST-21-0  iii      110  case
#> CCMD13071240ST-21-0   ii      126  case
#> CCMD13934959ST-21-0   ii      100  case
#> CCMD14479708ST-21-0   iv      110  case
#> CCMD18872694ST-21-0  iii      145  case