Result class returned by svaEnmix

Objects of class "dnaEPICO_svaEnmix" are list-based results returned by svaEnmix(). They collect the loaded inputs, surrogate-variable results, association-analysis summaries, and optional file outputs.

Structure

targets

Phenotype table read from phenoFile after any optional row subsetting.

RGSet

Loaded RGChannelSet with sample names reset to match targets.

svaData

Object returned by estimateSvaEnmixControls().

mergedPheno

Phenotype table returned by mergeSvaTargetsEnmix() after surrogate variables were appended.

analysisData

Object returned by analyzeSvaEnmix().

plotFiles

Named list of TIFF output paths for the SVA figures when saveOutputs = TRUE, otherwise NULL entries for plots not written.

savedFiles

Object returned by writeSvaEnmixOutputs() when saveOutputs = TRUE, otherwise NULL.

logFile

Resolved path to the optional log file, or NULL when logging was disabled.

See also

svaEnmix()