MSpecificCoxPh {MicrobiomeSurv}

Taxon by taxon Cox proportional analysis

Description

The Function fits cox proportional hazard model and does classification for each taxon separately

Usage

MSpecificCoxPh(
  Survival,
  Micro.mat,
  Censor,
  Reduce = FALSE,
  Select = 5,
  Prognostic = NULL,
  Mean = TRUE,
  Quantile = 0.5,
  Method = "BH"
)

Arguments

Survival

A vector of survival time with length equals to number of subjects

Micro.mat

A large or small microbiome profile matrix. A matrix with microbiome profiles where the number of rows should be equal to the number of taxa and number of columns should be equal to number of subjects.

Censor

A vector of censoring indicator.

Reduce

A boolean parameter indicating if the microbiome profile matrix should be reduced, default is TRUE and larger microbiome profile matrix is reduced by supervised pca approach.

Select

Number of taxa (default is 5) to be selected from supervised PCA. This is valid only if the argument Reduce=TRUE.

Prognostic

A dataframe containing possible prognostic(s) factor and/or treatment effect to be used in the model.

Mean

The cut off value for the classifier, default is the mean cutoff.

Quantile

If users want to use quantile as cutoff point. They need to specify Mean = FALSE and a quantile that they wish to use. The default is the median cutoff.

Method

Multiplicity adjustment methods.

Details

This function fits taxon by taxon Cox proportional hazard model and perform the classification based on a microbiome risk score which has been estimated using a single taxon. Function is useful for majority vote classification method and taxon by taxon analysis and also for top K taxa.

Value

A object of class ms is returned with the following values

Result

The cox proportional regression result for each taxon

HRRG

The hazard ratio statistics (Hazard-ratio, Lower confidence interval and upper confidence interval) of the riskgroup based on the riskscore and the cut off value for each taxon

Group

The classification of the subjects based on each taxon analysis

Mi.names

The names of the taxa for the analysis

Author(s)

Thi Huyen Nguyen, [e-mail]

Olajumoke Evangelina Owokotomo, [e-mail]

Ziv Shkedy

See Also

coxph, EstimateHR

Examples

# Prepare data
data(Week3_response)
Week3_response = data.frame(Week3_response)
surv_fam_shan_w3 =
data.frame(cbind(as.numeric(Week3_response$T1Dweek), as.numeric(Week3_response$T1D)))
colnames(surv_fam_shan_w3) = c("Survival", "Censor")
prog_fam_shan_w3 = data.frame(factor(Week3_response$Treatment_new))
colnames(prog_fam_shan_w3) = c("Treatment")
data(fam_shan_trim_w3)
names_fam_shan_trim_w3 =
c("Unknown", "Lachnospiraceae", "S24.7", "Lactobacillaceae", "Enterobacteriaceae", "Rikenellaceae")
fam_shan_trim_w3 = data.matrix(fam_shan_trim_w3[ ,2:82])
rownames(fam_shan_trim_w3) = names_fam_shan_trim_w3
# Using the function
Cox_taxon_fam_shan_w3 = MSpecificCoxPh(Survival = surv_fam_shan_w3$Survival,
                                      Micro.mat = fam_shan_trim_w3,
                                      Censor = surv_fam_shan_w3$Censor,
                                      Reduce=FALSE,
                                      Select=5,
                                      Prognostic = prog_fam_shan_w3,
                                      Mean = TRUE,
                                      Method = "BH")

# Results
show(Cox_taxon_fam_shan_w3)
summary(Cox_taxon_fam_shan_w3)