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.