run_contrast_2_levels: Extract DESeq2 results

Description Usage Arguments Value Examples

Description

Extract differential results for two classes from DESeq2 results object.

Usage

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

Arguments

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.

Value

Returns a list containing the following:

Examples

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## 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)

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