Identify DE genes.

Identify DE genes.

findDEGs(x, ...)

# S4 method for DGEList
findDEGs(x, test, design, contrasts, coefs, sample_meta, lfc = log2(2))

# S4 method for BbcSE
findDEGs(
  x,
  de_pkg = "edger",
  test = "glmQLFTest",
  design,
  contrasts = NULL,
  coefs = NULL,
  lfc = log2(2)
)

Arguments

x

A BbcSE object or a DGEList or a DESeqDataSet.
...

Not used currently.
test

For de_pkg="edger", either "glmQLFTest" or "glmTreat"
design

chr value. For example, '~0+group'. Variables in the design must be present in colData. For de_pkg="edger", passed to glmQLFit
contrasts

list of chr vectors containing variable name, numerator level, denominator level. For nested contrasts, use the format 'level2-level1' for the numerator and denominator values.
coefs

list of integers or character vectors indicating which coefficients of the linear model are to be tested equal to zero. Values must be columns or column names of design.
sample_meta

Column meta data as DataFrame or data.frame
lfc

See edgeR::glmTreat. Only used for test="glmTreat".
de_pkg

"edger" or "deseq2". Only used if x is a BbcSE

Value

A BbcSE object or a BbcEdgeR object or...

Details

Uses methods from the package corresponding to the de_pkg paramter:

edger

Uses edgeR::glmQLFit folllowed by either glmQLFTest or glmTreat

deseq2

Not implemented yet.

Methods (by class)

  • DGEList: Run glmQLFTest or glmTreat. Accepts contrasts in the format (a matrix) produced by limma::makeContrasts

  • BbcSE: Run edgeR or DESeq2 DE testing workflows.

See also

glmQLFit glmQLFTest glmTreat