findDEGs: Identify DE genes.

In vari-bbc/bbcRNA: Bulk RNA-seq workflow for VAI BBC

Description

Identify DE genes.

Usage

findDEGs(x, ...)

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

## S4 method for signature '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

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.

Value

A BbcSE object or a BbcEdgeR object or...

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

vari-bbc/bbcRNA documentation built on Nov. 10, 2020, 11:09 p.m.