SummarizedPhyloStats-class: S4 class SummarizedPhyloStats

In zhuchcn/phylox: Analyzing and Visualization Microbiome Data on Different Phylogenic Levels

Description

A S4 object to store hypothesis test statistical results of phylogenic sequencing experiment data, at different phylogenic level

Details

This class has 8 slots and each stores the hypothesis test statistical results of a designated phylogenic level, from otu to kingdom.There are currently two statistical packages supported, limma and DESeq2. There are 2 construction methods spy_to_deseq2 and spy_to_limma. The purpose of this class is to allow users to conduct hypothesis test using DESeq2 or limma at all phylogenic levels and view the results quickly.

This class has 8 slots and each slot is a data.frame with 5 variables as below:

baseMean

The mean value of the baseline group. This corresponds to the AveExpr from the limma result or the baseMean from the DESeq2 result

logFC

Log transformed fold change from baseline. This corresponds to the logFC from the limma result or the log2FoldChange from the DESeq2 result

stat

The statistic value. This corresponds to the t from the limma result or the stat from the DESeq2 result

pvalue

The raw p-value. This corresponds to the P.Value from the limma result or the pvalue from the DESeq2 result

padj

The adjusted p-value. This corresponds to the adj.P.Value from the limma result or the padj from the DESeq2 result

Slots

kingdom_table

Summarized statistic result at kingdom level.

phylum_table

Summarized statistic result at phylum level.

class_table

Summarized statistic result at class level.

order_table

Summarized statistic result at order level.

family_table

Summarized statistic result at family level.

genus_table

Summarized statistic result at genus level.

species_table

Summarized statistic result at species level.

otu_table

Summarized statistic result at otu level.

Author(s)

Chenghao Zhu

See Also

spy_to_deseq2 spy_to_limma summarizeFromPhyloseq SummarizedPhyloseq-accessors SummarizedPhyloseq-assign phyloseq-class

zhuchcn/phylox documentation built on May 31, 2019, 5:14 p.m.