merge_results.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/merge_results.R
\name{merge_results}
\alias{merge_results}
\title{Gather enrichment results}
\usage{
merge_results(
  MAGMA_results,
  level = 1,
  dataset_name = NULL,
  species = "mouse",
  filetype = "ctAssocMerged",
  q_thresh = NULL,
  method = "fdr",
  save_dir = tempdir(),
  verbose = TRUE
)
}
\arguments{
\item{MAGMA_results}{The output of
\link[MAGMA.Celltyping]{celltype_associations_pipeline}.}

\item{level}{Which level in the CellTypeDataset (CTD) to show results for.}

\item{dataset_name}{[Optional] Name of the CellTypeDataset (CTD).}

\item{species}{Species that the CellTypeDataset (CTD) came from.}

\item{filetype}{Type of analysis to gather the results of.
These correspond to the modes of data analysis in 
\link[MAGMA.Celltyping]{celltype_associations_pipeline}:
\itemize{
\item{\code{"ctAssocsLinear"} : }{Linear mode results.}  
\item{\code{"ctAssocsTop"} : }{Top 10\% mode results.}  
\item{\code{"ctAssocMerged"} : }{Merged linear and top 10\% results.}  
\item{\code{"ctCondAssocs"} : }{Conditional results.}  
}  

\emph{Note:} Only those analyses that were actually run in 
\link[MAGMA.Celltyping]{celltype_associations_pipeline} can be retrieved.}

\item{q_thresh}{Multiple-testing corrected p-value (q-value) 
filtering threshold.}

\item{method}{correction method, a \code{\link{character}} string.
    Can be abbreviated.}

\item{save_dir}{Directory to save the gathered results to.}

\item{verbose}{Print messages.}
}
\description{
Gather enrichment results from 
\link[MAGMA.Celltyping]{celltype_associations_pipeline} and converted them 
into harmonised, machine-readable tables.
}
\examples{
\dontrun{
#### Use precomputed results: see ?enrichment_results for details  ####
MAGMA_results <- MAGMA.Celltyping::enrichment_results

#### Merge results ####
merged_res <- MAGMA.Celltyping::merge_results(MAGMA_results)
}
}