run_contrast_2_levels: Extract DESeq2 results

Description Usage Arguments Value Examples

View source: R/diff_tests.R

Description

Extract differential results for two classes from DESeq2 results object.

Usage

1
2
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

1
2
3
4
5
6
## 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 April 19, 2018, 12:25 a.m.