Takes Utility_Coereba output, plus additional metadata,and returns as a Bioconductor Summarized Experiment object

Takes Utility_Coereba output, plus additional metadata,and returns as a Bioconductor Summarized Experiment object

Usage

Coereba_Processing(
  x,
  themetadata = NULL,
  metadata_columns = NULL,
  metadataTemplate = FALSE,
  outpath = NULL,
  panel,
  SpecimenVariable = "specimen",
  ClusterVariable = "Cluster"
)

Arguments

x

An object with Coereba gating and metadata. Acccepted arguments include a file.path to an .fcs, a flowFrame or cytoFrame, and a data.frame.

themetadata

A data.frame or file.path to a metadata.csv file

metadata_columns

A vector of column names from the metadata want to incorporate.

metadataTemplate

When metadata is NULL, returns a template data.frame containing specimen list.

outpath

Default NULL, alternate a file.path to send metadataTemplate output to.

panel

A data.frame or file.path to a .csv containing Fluorophore and Marker columns

SpecimenVariable

Column designating specimen in the metadata, default "specimen"

ClusterVariable

Column designating specimen in the metadata, default "Cluster"

Value

A summarized experiment object

Examples

library(Coereba)