run_contrast_2_levels: Extract DESeq2 results
In TBrach/MicrobiomeX: eXtended Functions for Microbiome Analysis and Visualization

Description Usage Arguments Value Examples

Extract differential results for two classes from DESeq2 results object.

1 2	run_contrast_2_levels(dds, physeq, group, block = NULL, compare = NULL, cooksCutoff = TRUE)

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

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.

## Not run: 

res <- run_contrast_2_levels(dds, physeq, group = "Diet", compare=c("Control", "High_Fat"), block = "Gender")
res <- run_contrast_2_levels(dds, physeq, group = "Diet", compare=c("Control", "High_Fibre"), block = "Gender")

## End(Not run)