load_shared: Reads in a file containing OTU count data and keeps OTUs...

In cb-42/cbmbtools: R Functions for Facilitating Microbiome Analyses

Description

Reads in a file containing OTU count data and keeps OTUs which meet or exceed a specified % abundance in at least one sample.

Usage

load_shared(shared, otu_vec = NULL, thresh = 0.1)

Arguments

shared	An opti_mcc.shared file resulting from processing via mothur.
otu_vec	An optional vector containing OTUs to be excluded, prior to trimming. This could be obtained from extracting a subset of OTUs from the result of load_tax.
thresh	Threshold used to determine whether any OTUs should be trimmed from the dataset. If an OTU does not reach thresh at least once in a sample, the OTU will be removed. Default threshold is 0.1.

Value

Returns a matrix containing OTU counts, (optionally) without OTUs contained in otu_vec and also trimmed to remove OTUs that did not cross the specified percentage in at least one sample.

Examples

load_shared("miseq_mothur.shared", thresh = .05)

cb-42/cbmbtools documentation built on Jan. 9, 2021, 1:38 a.m.