drseqFit: DrSeq Fit
In fchen365/surf: Statistical Utility for RBP (RNA binding protein) Functions

Description Usage Arguments Details Value

Fit DrSeq models using the DEXSeq as the estimation engine.

drseqFit(
  drd,
  fullModel = design(drd@drseqData),
  reducedModel = ~sample + exon,
  fitExpToVar = "condition",
  cores = max(1, detectCores() - 2),
  verbose = FALSE
)

`drd`	a `surf` object from drseqCount.
`fullModel`	The full model formula
`reducedModel`	Null model formula.
`fitExpToVar`	A variable name contained in the sample data. The expression values will be fitted to this variable using the the formula " ~ sample + fitExpToVar * exon".
`cores`	`integer`, number of computing workers.
`verbose`	`logical`, whether (`TRUE`) to echo progress.

the drseqResults slot contains extensive DrSeq results. To access the object, use drseqResults function.

a surf object with (1) drseqResults and sampleData slot updated and (2) three added columns:

`eventBaseMean`	base read coverage of the event from RNA-seq data.
`padj`	adjusted p-value for differential REU.
`logFoldChange`	estimated log2 fold change of REU: log2(condition of the 1st sample / another condition)