reconcile_categories: Cleans absent levels in sample_data/data.frame.

In phyloseq: Handling and analysis of high-throughput microbiome census data

Description

This is used internally by the builder method, sample_data, to ensure that the factors describing categorical variables in a data.frame or sample_data object are free of extra levels that can plague downstream plots analysis.

Usage

reconcile_categories(DFSM)

Arguments

DFSM	(Required). A data.frame or sample_data object that needs to be cleaned.

Value

A single data.frame object. Even if the input argument is a sample_data, the return is a data.frame. Because this is intended to be used internally by the builder method, it cannot also call the builder function to re-build the cleaned sample_data.

Examples

# # # data(GlobalPatterns)
# # # SM <- sample_data(GlobalPatterns)
# # # DF <- data.frame(SM)
# # # DF <- data.frame(DF, col1=1:nrow(DF), col2=paste(1:nrow(DF), "t", sep=""))
# # # DF <- reconcile_categories(DF)
# # # SM <- sample_data(reconcile_categories(SM))
# # # sapply(DF, class)
# # # sapply(SM, class)

Example output

phyloseq documentation built on Nov. 8, 2020, 6:41 p.m.