build_DAF_data: Load all data for DAF analysis

In LeoStafu/metaDAF: Metagenomics tools for detecting Differentially Abundant Features

Description

Create a list that will contain all data needed for differential features analysis.

Usage

build_DAF_data(count_table, metadata, group_var = NULL,
  simulation = TRUE, ...)

Arguments

count_table	a matrix of count values with features as rows and samples as columns.
metadata	a data frame. Rows are samples and miscellaneous variables as columns.
group_var	character. The name of metadata column defining the groups.
simulation	logical. Should differences be generated ? Default is TRUE.
...	additionnal parameter passed to the generateData function

Details

If the columns names of the count table do not match the rows names of the metadata table, metadata columns are screened for a variable countaining these names.

If such variable is not found, it is assumed that individuals follow the same order through count table columns and metadata rows.

Value

a list of 2 or 4 elements :

count_table	a matrix of count values.
metadata	a data frame of at least one column countaining the group variable.

If the simulation parameter was TRUE, artificial differences were generated. It is possible to know exactly which are the true differentially abundant features (DAF).

true_DAF	a character vector. The names of the true DAF.
FC_true_DAF	a numeric vector. The fold-change of the true DAF.

LeoStafu/metaDAF documentation built on July 14, 2019, 6:41 p.m.