README.md

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

filtR

filtR is an R package developed to filter operational taxonomic units (OTUs) or amplicon sequence variants (ASVs) from count tables if they are determined to be generated by sequencing error and/or PCR error.

The filtR R package currently contains a single function, filtR().

For an in-depth tutorial of the package, use browseVignettes("filtR") within R.

Installation

Use the devtools R package to install from this GitHub repository:

devtools::install_github('bjoris33/filtR') NOTE: You may need to restart R after installing.

Software Requirements

filtR was developed on R version 3.5.0, so it is recommended to use the same version or higher to avoid any compatibility issues.

Additionally two separate R packages are required for filtR:

propr -- Version 3.5.1 was used for the development of filtR.

ALDEx2 -- Version 1.12.0 was used for the development of filtR.

Data Input

filtR reads a locally stored count table from the count_file = term within the function. The count table must be formatted with samples as columns and OTUs/ASVs as rows. Count tables with and without columns for taxonomy are supported by filtR.

Data Output

filtR returns to its assigned variable a count table in the same format as the original table, less the rows (OTUs/ASVs) that filtR determined to be error-derived.

Filtering Parameters

rho_CO: Defaults to 0.7. Range 0 to 1. rho is a statistic can be used to assess beta-association between a pair of features. As the value of rho approaches 1, it can be assumed that the two features used to calculate rho have a constant ratio across the dataset and are therefore associated. The premise of ASVs and OTUs is generally that each individual ASV and OTU, for the most part, should lack association with other ASVs/OTUs because they are independent entities. Error-derived OTUs/ASVs will occur as a constant ratio of the OTU they are derived from and therefore will have a high rho value.

clr_CO: Defaults to 5 and can be assigned any value greater than 0. If an OTU/ASV is error-derived, it will not only have a high rho value, it will also have a high difference in centered log ratio compared to the OTU/ASV it is derived from. It is not recommended that this cutoff be set lower than 5.

Data Visualization

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.

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