Run.DESeq2: Prepare and Run DESeq

In goushixue/QRseq: Quickly RNA-seq Analysis Platform

Prepare and Run DESeq

Description

Prepare and Run DESeq

Usage

Run.DESeq2(
  expr.data,
  sample.data,
  formula,
  test,
  fitType,
  sfType,
  betaPrior,
  reduced,
  minReplicatesForReplace,
  modelMatrixType,
  useT,
  minmu
)

Arguments

expr.data	expression matrix
sample.data	sample infomation meta data
formula	experiment design formula
test	either "Wald" or "LRT", which will then use either Wald significance tests (defined by nbinomWaldTest), or the likelihood ratio test on the difference in deviance between a full and reduced model formula (defined by nbinomLRT)
fitType	either "parametric", "local", or "mean" for the type of fitting of dispersions to the mean intensity.
sfType	either "ratio", "poscounts", or "iterate" for teh type of size factor estimation.
betaPrior	whether or not to put a zero-mean normal prior on the non-intercept coefficients
reduced	for test="LRT", a reduced formula to compare against
minReplicatesForReplace	the minimum number of replicates required in order to use replaceOutliers on a sample.
modelMatrixType	either "standard" or "expanded", which describe how the model matrix, X of the GLM formula is formed.
useT	logical, passed to nbinomWaldTest, default is FALSE, where Wald statistics are assumed to follow a standard Normal
minmu	lower bound on the estimated count for fitting genewise dispersion and for use with nbinomWaldTest and nbinomLRT

goushixue/QRseq documentation built on July 9, 2023, 9:28 a.m.