filtR: Filters OTUs Generated by PCR or Sequencing Error from Count...

In bjoris33/filtR: Filters OTUs Generated by PCR or Sequencing Error from Count Tables

Description

Using propr and ALDEx2 functions, filtR removes OTUs generated by PCR and sequencing error from count tables. The input for this package is a count table with the columns as samples and the rows as OTUs/ASVs.

Usage

filtR(count_file, rho_CO = 0.7, clr_CO = 5, plot = FALSE)

Arguments

count_file	Input your saved count table file.
rho_CO	Input your rho value cutoff. Range of 0 to 1. Higher value results in a tighter filter with fewer OTUs being discarded. Defaults to 0.7.
clr_CO	Input your centered log ratio difference cutoff. Higher value results in a tighter filter with fewer OTUs being discarded. Defaults to 5.
plot	Set to TRUE to create scatter plots of the CLRs of the filtered OTU plotted against the CLRs of the OTU from which they are derived. The black, solid line is the ideal slope of the line for association (slope of 1) and the red dashed line is the slope of the linear model of the data. Defaults to FALSE.

Value

Count table with error-derived OTUs removed.

Examples

function(count_file='SRP058027_taxonomy_abundances_SSU_v4.1.tsv', rho_CO=0.7, clr_CO=5, plot=TRUE)

bjoris33/filtR documentation built on May 31, 2019, 7:40 a.m.