MiFreq {MicrobiomeSurv}

Frequency of Selected Taxa from the LASSO, Elastic-net Cross-Validation

Description

The function selects the frequency of selection from the shrinkage method (LASSO, Elastic-net) based on cross validation, that is the number of times each taxon occur during the cross-validation process. This function outputs the mostly selected taxa during the LASSO and Elastic-net cross validation. Selected top taxa are ranked based on frequency of selection and also a particular frequency can be selected. In addition, it visualizes the selected top taxa based on the minimum frequency specified.

Usage

MiFreq(Object, TopK = 20, N = 3)

Arguments

Object

An object of class cvle returned from the function CVLasoelascox.

TopK

The number of Top K taxa (5 by default) to be displayed in the frequency of selection graph.

N

The taxa with the specified frequency should be displayed in the frequency of selection graph.

Value

A vector of taxa and their frequency of selection. Also, a graphical representation is displayed.

Author(s)

Thi Huyen Nguyen, [e-mail]

Olajumoke Evangelina Owokotomo, [e-mail]

Ziv Shkedy

See Also

cvmm, coxph, EstimateHR, CVLasoelascox

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$Treatment_new))
colnames(prog_fam_shan_w3) = c("Treatment")
data(fam_shan_trim_w3)
names_fam_shan_trim_w3 =
c("Unknown", "Lachnospiraceae", "S24.7", "Lactobacillaceae", "Enterobacteriaceae", "Rikenellaceae")
fam_shan_trim_w3 = data.matrix(fam_shan_trim_w3[ ,2:82])
rownames(fam_shan_trim_w3) = names_fam_shan_trim_w3
# Cross-Validation for LASSO and ELASTIC-NET
CV_lasso_fam_shan_w3 = CVLasoelascox(Survival = surv_fam_shan_w3$Survival,
                                     Censor = surv_fam_shan_w3$Censor,
                                     Micro.mat = fam_shan_trim_w3,
                                     Prognostic = prog_fam_shan_w3,
                                     Standardize = TRUE,
                                     Alpha = 1,
                                     Fold = 4,
                                     Ncv = 10,
                                     nlambda = 100)


# Using the function
MiFreq_fam_shan_w3 = MiFreq(Object = CV_lasso_fam_shan_w3, TopK=5, N=3)