clean_shared: Reformat a shared file

In OTUtable: North Temperate Lakes - Microbial Observatory 16S Time Series Data and Functions

Description

Converts a mothur .shared file into a simplified OTU table. The columns indicating total reads for each OTU and the clustering level are removed, and the table is transposed so that OTUs are rows and samples are columns. The "trim.names" variable provides an option to shorten sample names to the first "." character - this is specific to the NTL-Microbial Observatory dataset. Manual curation of sample names took place after this step for the NTL-Microbial Observatory dataset in order to maintain consistency across all sample names.

Usage

clean_shared(shared_file, trim.names)

Arguments

shared_file	A .shared file output by mothur
trim.names	TRUE or FALSE - if TRUE, sample names will be trimmed to the first "." character.

Value

Returns an OTU table with samples as columns and OTUs as rows.

Author(s)

Alexandra Linz <[e-mail]>

Examples

# Example path only: path <- "mothur_output/bogs.shared"

# otu_table <- clean_shared(path, trim.names = T)
# write.csv(otu_table, file = "bogs_otu_table.csv", quote = F, row.names = T)

OTUtable documentation built on May 1, 2019, 10:51 p.m.