Filter_function: Filter OTU/ASV/metagenomic profile/gene profile by threshold

In LorMe: Lightening One-Code Resolving Microbial Ecology Solution

Filter OTU/ASV/metagenomic profile/gene profile by threshold

Description

Sequenced data of taxonomy&gene still remains some sequencing error which we needed to be wiped off before analyzing. Here we provide function including four formats to wipe them clean.

Usage

Filter_function(input, threshold, format, report = TRUE)

Arguments

input	Data frame of absolute abundance of standard OTU table,with the first column of OTUID and the final column of taxonomy annotation. If your data frame is gene table or not a standard OTU table, please manually transformed into a standard input data frame.
threshold	threshold of filter.Relative abundance for format 1 and 4, reads number for format 2, sample size for format 3
format	1:filter OTU/gene below overall-sample relative abundance threshold(<) 2:filter OTU/gene below overall-sample reads threshold(<) 3:filter OTU/gene reads 0 over threshold sample size(>) 4:filter OTU/gene below relative abundance threshold in each sample(<)
report	Logical. If print report to console. Default:TRUE

Value

Dataframe of OTU/gene in format of absolute abundacne(reads) or relative abundance(%)

Author(s)

Wang Ningqi

Examples

### Data frame with absolute abundance (reads)###
### And first column of OTUID and last column of taxonomy ###
data(testotu)

#### If your data frame does not contain the OTUID column or taxonomy column,
#### you can add a simulated column to fit the input format like testotu ##

### 1. Filter OTU with total relative abundance below 0.0001###
filtered_otu <- Filter_function(
  input = testotu,
  threshold = 0.0001,
  format = 1
)

### 2. Filter OTU with total reads below 20 ###
filtered_otu <- Filter_function(
  input = testotu,
  threshold = 20,
  format = 2
)

### 3. Filter OTU reads 0 over (>=) 11 samples ###
filtered_otu <- Filter_function(
  input = testotu,
  threshold = 11,
  format = 3
)

### 4. Filter OTU with relative abundance below 0.0001 in each sample ###
filtered_otu <- Filter_function(
  input = testotu,
  threshold = 0.0001,
  format = 4
)

LorMe documentation built on Sept. 13, 2024, 9:07 a.m.