Read.Filter: Read.Filter

In jbisanz/MicrobeR: Handy functions for microbiome analysis in R

Description

Remove samples with less than a user specified number of reads.

Usage

filter<-Read.Filter(svtable, metadata, 5000)
newtable<-filter$Features
newmetadata<-filter$Metadata

Arguments

FEATURES	Table of feature/OTU/SV counts where Samples are columns, and IDs are row names.
METADATA	Metadata file where samples are row names.
READCUTOFF	Minimum number of reads to pass filter
VERBOSE	Should lists of which samples were removed or kept be printed to screen? (defaults to TRUE)
PLOT	Should a plot of read depth be made? (defaults to TRUE)

Value

A named list containing new feature table and metadata.

jbisanz/MicrobeR documentation built on June 5, 2019, 7:53 p.m.