test_differential_abundance_DESeq2: DESeq2 - negative binomial Wald test

In TBrach/MicrobiomeX: eXtended Functions for Microbiome Analysis and Visualization

Description

Run negative binomial Wald test using DESeq2 on all taxa in a phylseq object. If block is specified, then it is used as an additional factor. If block is NULL, then standard test is used.

Usage

test_differential_abundance_DESeq2(physeq, group, compare = NULL,
  block = NULL, cooksCutoff = TRUE)

Arguments

physeq	Phyloseq object.
group	Name of column in sample metadata to perform group-wise comparisons on.
compare	List of 2 groups to be compared, which are present in the group column.
block	Name of column in sample metadata to control for the group-wise comparisons.
cooksCutoff	Cook's cutoff passed on to contrast() function in DESeq2.

Value

Returns a list containing the following:

• table: data frame containing the negative binomial Wald test results from DESeq2, with the following columns:
  Taxon, teststat, pvalue, padj, significance, direction, Mean_grp1, Mean_grp2, baseMean, log2FC, tax_table(phyloseq).

• dds: raw analysis results from DESeq2.

• physeq_adj: adjusted counts from DESeq2.

• test_name: Name of test used - in this case "Negative binomial Wald test".

• block : Name of variable used as blocking factor.

Examples

## Not run: 

# If there are only 2 levels for \code{Diet}
res <- test_differential_abundance_DESeq2(physeq, group = "Diet", block = "Gender")

# If there are multiple levels for \code{Diet}
res <- test_differential_abundance_DESeq2(physeq, group = "Diet", compare=c("Control", "High_Fat"), block = "Gender")
res <- test_differential_abundance_DESeq2(physeq, group = "Diet", compare=c("Control", "High_Fibre"), block = "Gender")

## End(Not run)

TBrach/MicrobiomeX documentation built on May 14, 2019, 2:28 p.m.