DA.ds2x: DESeq2

View source: R/DA.ds2x.R

DA.ds2xR Documentation

DESeq2

Description

Implementation of DESeq2 for DAtest

Usage

DA.ds2x(
  data,
  predictor,
  paired = NULL,
  covars = NULL,
  out.all = NULL,
  p.adj = "fdr",
  coeff = 2,
  coeff.ref = 1,
  allResults = FALSE,
  ...
)

Arguments

data

Either a matrix with counts/abundances, OR a phyloseq object. If a matrix/data.frame is provided rows should be taxa/genes/proteins and columns samples

predictor

The predictor of interest. Either a Factor or Numeric, OR if data is a phyloseq object the name of the variable in sample_data(data) in quotation

paired

For paired/blocked experimental designs. Either a Factor with Subject/Block ID for running paired/blocked analysis, OR if data is a phyloseq object the name of the variable in sample_data(data) in quotation

covars

Either a named list with covariables, OR if data is a phyloseq object a character vector with names of the variables in sample_data(data)

out.all

If TRUE, will run "LRT" which will produce one p-value for the predictor. If FALSE will run "Wald" test and will output p-value from one level of the predictor specified by coeff. If NULL (default) set as TRUE for multi-class predictor and FALSE otherwise

p.adj

Character. P-value adjustment. Default "fdr". See p.adjust for details

coeff

Integer. The log2FoldChange (and p-value if test="Wald") will be associated with this coefficient. This coefficient is by default compared to the intercept (1. level of predictor), change this with coeff.ref. Default 2, i.e. the 2. level of the predictor.

coeff.ref

Integer. Reference level of the predictor. Default the intercept, = 1

allResults

If TRUE will return raw results from the DESeq function

...

Additional arguments for the DESeq function

Value

A data.frame with with results.

Examples

# Creating random count_table and predictor
set.seed(6)
mat <- matrix(rnbinom(200, size = 0.2, mu = 500), nrow = 20, ncol = 10)
rownames(mat) <- 1:20
pred <- c(rep("Control", 5), rep("Treatment", 5))

# Running DESeq2
res <- DA.ds2x(data = mat, predictor = pred)

Russel88/DAtest documentation built on March 24, 2022, 3:50 p.m.