methodWrapper.DESeq2: DESeq2

In jhsiao999/ashbun: Methods and evaluation tools for single cell RNA-seq count data

Description

Implement DESeq2.

Usage

methodWrapper.DESeq2(counts, condition, libsize_factors = NULL,
  control = list(save_modelFit = FALSE, independentFiltering = FALSE,
  cooksCutoff = FALSE))

Arguments

counts	Gene by sample expression count matrix (G by N).
condition	Binary vector of length N indicating sample biological condition.
libsize_factors	Numeric vector of scale factors for library sizes. Default NULL computes libsize_factors using DESeq2.
control	A list with control arguments, including save_modelFit TRUE to output the complete DESeq2 fit results. independentFiltering DESeq2 internal argument. Default = FALSE to not apply gene filtering. cooksCutoff DESeq2 internal argument. Default = FALSE to not exclude samples.

Value

List with the following objects betahat Estimate effect size of condition for all genes. sebetahat Standard errors of the effect sizes. pvalue P-values of the effect sizes. fit DESeq2 complete output of the model fit. NULL if save_modelFit = FALSE.

Author(s)

Chiaowen Joyce Hsiao

jhsiao999/ashbun documentation built on May 8, 2019, 11:17 p.m.