formatDataSets: Format Data

In HMP: Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP

Description

For a list of datasets, this function finds the union of taxa across all datasets and transforms them such that they all have the same columns of taxa.

Usage

formatDataSets(group.data)

Arguments

group.data

A list where each element is a matrix of taxonomic counts(columns) for each sample(rows). Note that the row names should correspond to sample names

Details

This function will also sort all the columns into the same order for every dataset and remove any columns that have 0's for every sample.

E.g. For two datasets, any taxa present in dataset1 but not dataset2 will be added to dataset2 with a 0 count for all samples and vice versa.

Value

The list given, but modified so every data set has the same ordering and number of columns

Examples

	data(saliva)
	data(throat)
	
	### Set each data set to have 10 different columns
	saliva2 <- saliva[,1:10]
	throat2 <- throat[,11:20]
	
	### Combine the data sets into a single list
	group.data <- list(saliva2, throat2)
	
	formattedData <- formatDataSets(group.data)
	formattedData[[1]][1:5, 1:5]

HMP documentation built on Aug. 31, 2019, 5:05 p.m.