PreFL: Prefiltering for Microbiome Data

In EvaYiwenWang/PLSDAbatch: PLSDA-batch

Prefiltering for Microbiome Data

Description

This function prefilters the data to remove samples or microbial variables with excess zeroes.

Usage

PreFL(data, keep.spl = 10, keep.var = 0.01)

Arguments

data	The data to be prefiltered. The samples in rows and variables in columns.
keep.spl	The minimum counts of a sample to be kept.
keep.var	The minimum proportion of counts of a variable to be kept.

Value

PreFL returns a list that contains the following components:

data.filter	The filtered data matrix.
sample.idx	The indexs of samples kept.
var.idx	The indexs of variables kept.
zero.prob	The proportion of zeros of the input data.

Author(s)

Yiwen Wang, Kim-Anh Lê Cao

References

\insertRef

le2016mixmcPLSDAbatch

Examples

library(TreeSummarizedExperiment) # for functions assays()
data('AD_data')

ad.count <- assays(AD_data$FullData)$Count # microbial count data
ad.filter.res <- PreFL(data = ad.count)

# The proportion of zeroes of the AD count data
ad.zero.prob <- ad.filter.res$zero.prob

# The filtered AD count data
ad.filter <- ad.filter.res$data.filter

EvaYiwenWang/PLSDAbatch documentation built on Sept. 25, 2024, 8:54 p.m.