R: Biomarker Validation for Microbiome-Based Survival Classification and Prediction

# Biomarker Validation for Microbiome-Based Survival Classification and Prediction

## Documentation for package ‘MicrobiomeSurv’ version 0.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

CoxPHUni | This function will fit the full and reduced models and calculate LRT raw p-value and adjusted p-value based on BH Method
CVLasoelascox | Cross Validations for Lasso Elastic Net Survival predictive models and Classification
cvle | The cvle Class.
cvle-class | The cvle Class.
cvle-method | The cvle Class.
CVMajorityvotes | Cross validation for majority votes
cvmm | The cvmm Class.
cvmm-class | The cvmm Class.
cvmm-method | The cvmm Class.
CVMSpecificCoxPh | Cross validation for the Taxon specific analysis
cvmv | The cvmv Class.
cvmv-class | The cvmv Class.
cvmv-method | The cvmv Class.
CVPcaPls | Cross Validations for PCA and PLS based methods
cvpp | The cvpp Class.
cvpp-class | The cvpp Class.
cvpp-method | The cvpp Class.
cvsit | The cvsit Class.
cvsit-class | The cvsit Class.
cvsit-method | The cvsit Class.
CVSITaxa | Cross validation for sequentially increases taxa
data_zero_per_group_otu_w3 | Zero per treatment groups.
DistHR | Null Distribution of the Estimated HR
EstimateHR | Classification, Survival Estimation and Visualization
fam_info_w3 | Information at family level.
fam_shan_trim_w3 | Dataset at family level.
FirstFilter | This function is used for the first step of filtering which removes OTUs having all zeros (inactive OTUs). The input is an OTU matrix with rows are OTUs and columns are subjects.
GetRA | This function convert OTU matrix to RA matrix.
Lasoelascox | Wapper function for glmnet
Majorityvotes | Classifiction for Majority Votes
metadata_taxonomy | Metadata taxonomy.
MiFreq | Frequency of Selected Taxa from the LASSO, Elastic-net Cross-Validation
ms | The ms Class.
ms,ANY | The ms Class.
ms-class | The ms Class.
ms-method | The ms Class.
MSpecificCoxPh | Taxon by taxon Cox proportional analysis
perm | The perm Class.
perm-class | The perm Class.
perm-method | The perm Class.
plot-method | The cvle Class.
plot-method | The cvmm Class.
plot-method | The cvmv Class.
plot-method | The cvpp Class.
plot-method | The cvsit Class.
plot-method | The ms Class.
plot-method | The perm Class.
QuantileAnalysis | Quantile sensitivity analysis
SecondFilter | This function is used for the second step of filtering which removes OTUs based on a threshold.
show-method | The cvle Class.
show-method | The cvmm Class.
show-method | The cvmv Class.
show-method | The cvpp Class.
show-method | The cvsit Class.
show-method | The ms Class.
show-method | The perm Class.
SITaxa | Sequential Increase in Taxa for the PCA or PLS classifier
summary-method | The cvle Class.
summary-method | The cvmm Class.
summary-method | The cvmv Class.
summary-method | The cvpp Class.
summary-method | The cvsit Class.
summary-method | The ms Class.
summary-method | The perm Class.
SummaryData | This function gives indices such as Observed richness, Shannon index, Inverse Simpson, ... of higher level such as levelily, order, phylum, ...
SurvPcaClass | Survival PCA and Classification for microbiome data
SurvPlsClass | Survival PLS and Classification for microbiome data
Top1Uni | This function finds out the taxon has the smallest p-value, then calculate risk score of patients based on that taxon. Categorized subjects into high or low risk groups based on the mean of the risk score as a cutoff point Checking whether the two groups are significant difference in the probability to be survival.
Week3_otu | OTU table at week 3.
Week3_response | Response datase.
ZerosPerGroup | This function returns a matrix with rows are Micros and 9 columns containing number and the proportion of zeros per groups of treatments and in total.