CoxPHUni {MicrobiomeSurv}

This function will fit the full and reduced models and calculate LRT raw p-value and adjusted p-value based on BH Method

Description

This function will fit the full and reduced models and calculate LRT raw p-value and adjusted p-value based on BH Method

Usage

CoxPHUni(Survival, Censor, Prognostic, Micro.mat, Method = "BH")

Arguments

Survival

The time to event outcome.

Censor

An indicator variable indicate the subject is censored or not.

Prognostic

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

Micro.mat

a microbiome matrix, can be at otu, family or any level of the ecosystem. Rows are taxa, columns are subjectsc.

Method

A multiplicity adjustment Method that user can choose. The default is BH Method.

Value

A relative abundance matrix of OTUs

coef

coefficient of one microbiome (OTU or family, ...)

exp.coef

exponential of the coefficient

p.value.LRT

raw LRT p-value

p.value

adjusted p-value based on chosen Method

Author(s)

Thi Huyen Nguyen, [e-mail]

Olajumoke Evangelina Owokotomo, [e-mail]

Ziv Shkedy

See Also

CoxPHUni

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$Treatment_new))
colnames(prog_fam_shan_w3) = c("Treatment")
data(fam_shan_trim_w3)
names_fam_shan_trim_w3 =
c("Unknown", "Lachnospiraceae", "S24.7", "Lactobacillaceae", "Enterobacteriaceae", "Rikenellaceae")
fam_shan_trim_w3 = data.matrix(fam_shan_trim_w3[ ,2:82])
rownames(fam_shan_trim_w3) = names_fam_shan_trim_w3
# Using the funtion
summary_fam_shan_w3 = CoxPHUni(Survival = surv_fam_shan_w3$Survival,
                               Censor = surv_fam_shan_w3$Censor,
                               Prognostic = prog_fam_shan_w3,
                               Micro.mat = fam_shan_trim_w3,
                               Method = "BH")