summary-pmartRseq: Produce a basic summary of an pmartRseq S3 Object

In pmartR/pmartRseq: Analysis and Visualization of 16S Data

Description

This function will provide basic summary statistics about an object of the class seqData.

Usage

## S3 method for class 'seqData'
summary(omicsData)

## S3 method for class 'countSTAT_results'
summary(pmartRseq_results)

## S3 method for class 'alphaRes'
summary(pmartRseq_results)

## S3 method for class 'evenRes'
summary(pmartRseq_results)

## S3 method for class 'richRes'
summary(pmartRseq_results)

## S3 method for class 'abunRes'
summary(pmartRseq_results)

## S3 method for class 'jaccardRes'
summary(pmartRseq_results)

## S3 method for class 'effspRes'
summary(pmartRseq_results)

## S3 method for class 'countFilter'
summary(pmartRseq_results, min_num = NULL)

## S3 method for class 'indspRes'
summary(pmartRseq_results)

## S3 method for class 'paRes'
summary(pmartRseq_results)

Arguments

omicsData	an object of the class 'seqData' created by as.seqData
min_num	An integer value specifying the minimum number of fn counts a feature must have to be kept for statistical analysis. If fn="percent", give the decimal number, not the percentage.

Value

a list of elements

• num.samps number of samples in e_data

• num.edata number of unique identifying features in e_data

• num.emeta number of unique identifying features in e_meta

• num_na number of observations equal to NA in e_data

• frac_na fraction of observations equal to NA in e_data

• num_zero number of observations equal to 0 in e_data

• frac_zero fraction of observations equal to 0 in e_data

Author(s)

Lisa Bramer, Kelly Stratton, Allison Thompson

Examples

## Not run: 
library(mintJansson)
data(rRNA_data)
summary(rRNA_data)

## End(Not run)

pmartR/pmartRseq documentation built on May 25, 2019, 9:20 a.m.