ExtractResult - convenience function to return statistics for downstream analysis functions such as FgseaList. Returns results from list of dream or lmFit results from those functions natively (use model.fit.list = list(fit)) or from scglmmr::RunVoomLimma and scglmmr::dreamMixedModel
Source:R/model_result_interaction.r
ExtractResult.RdExtractResult - convenience function to return statistics for downstream analysis functions such as FgseaList. Returns results from list of dream or lmFit results from those functions natively (use model.fit.list = list(fit)) or from scglmmr::RunVoomLimma and scglmmr::dreamMixedModel
Usage
ExtractResult(
model.fit.list,
what = c("statistics", "lmer.z.ranks", "gene.t.ranks")[1],
coefficient.number,
coef.name
)Arguments
- model.fit.list
list of model results indexed by celltypes returned by `scglmmr::dreamMixedModel`, `scglmmr::RunVoomLimma`, or manually by `lmFit` or `dream`.
- what
what to return what = c('statistics', 'lmer.z.ranks' or 'gene.t.ranks')[1] defaults to statistics for each cell type, e.g. avg exprs, logFC, t statistic, pval, adj.P.Val etc. If gene.z.ranks, ranks genes based on z statistic (mixed models) and returns a list (indexed by celltype of named numeric vector of genes ranked for FgseaList.
- coefficient.number
what coefficient to return -- this needs to be one of model.fit.list$coefficients: check the order of the coefficients. Results returned from dream include statistical contrasts and estimated coefficients from the model. If limma::contrasts.fit was used (e.g. if using do_contrast_fit = TRUE in RunVoomLimma), these 'coefficients' are results of the statistical contrast.
- coef.name
the name of the estimated coefficient for which results are being returned; if returning results from a statistical contrast e.g. limma::contrasts.fit() this will be the name of the contrast. If returning a model fit with the dream function, can also be contrast specified by from variancePartition::makeContrastsDream() or a fixed effect parameter that was included in the model.