read.fluidigm.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/Readers.R
\name{read.fluidigm}
\alias{read.fluidigm}
\title{Reads a Fluidigm Biomark (c. 2011) raw data file (or set of files)}
\usage{
read.fluidigm(
  files = NULL,
  metadata = NULL,
  header.size = 2,
  skip = 8,
  cycle.threshold = 40,
  metadataColClasses = NULL,
  meta.key = NULL,
  idvars = NULL,
  splitby = NULL,
  unique.well.id = "Chamber.ID",
  raw = TRUE,
  assay = NULL,
  geneid = "Assay.Name",
  sample = NULL,
  well = "Well",
  measurement = "X40.Ct",
  measurement.processed = "Ct",
  ncells = "SampleRConc"
)
}
\arguments{
\item{files}{A \code{character} vector of files to read.}

\item{metadata}{A \code{character} path and filename of a CSV file containing additional metadata about the samples}

\item{header.size}{A \code{numeric} indicating the number of lines in the header (default 2)}

\item{skip}{\code{numeric} how many lines to skip before reading (default 8)}

\item{cycle.threshold}{The maximum number of PCR cycles performed (default 40) \code{numeric}}

\item{metadataColClasses}{Optional \code{character} vector giving the column classes of the metadata file. See \link{read.table}.}

\item{meta.key}{Optional \code{character} vector that identifies the key column between the metadata and the fluidigm data}

\item{idvars}{Optional \code{character} vector that defines the set of columns uniquely identifying a well (unique cell, gene, and condition).}

\item{splitby}{Optional \code{character} that defines the column / variable used to split the resulting data into a list of SingleCellAssay, such that unique levels of \code{splitby} each fall into their own SingleCellAssay. Ususally the experimental unit subjected to different treatments.}

\item{unique.well.id}{The column that uniquely identifies a sample well in the data. Default is "Chamber.ID".}

\item{raw}{\code{logical} flag indicating this is raw data coming off the instrument. Thus we make some assumptions about the column names that are present.}

\item{assay}{\code{character} name of a column that uniquely identifies an Assay (i.e. gene). Default is NULL}

\item{geneid}{\code{character} names of the column that identifies a gene. Default is "Assay.Name"}

\item{sample}{\code{character} name of a column that uniquely identifies a sample}

\item{well}{\code{character} name of a column that uniquely identifies a well. Default "Well".}

\item{measurement}{\code{character} name of the column that holds the measurement. Default "X40.Ct".}

\item{measurement.processed}{\code{character} one of "Ct","40-Ct", or "et". If not "Ct", the measurement will be transformed.}

\item{ncells}{The column with the number of cells in this well.}
}
\value{
list of \code{SingleCellAssay} holding the data.
}
\description{
This function reads a raw Fluidigm Biomark data file or set of files and constructs a SingleCellAssay (or FluigidmAssay) object.
This was written c. 2011 and has not been tested lately.  The Biomark format may have changed.
}
\author{
Greg Finak
}