read.fluidigm: Reads a Fluidigm Biomark (c. 2011) raw data file (or set of...
In MAST: Model-based Analysis of Single Cell Transcriptomics

Description Usage Arguments Value Author(s)

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.

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"
)

`files`	A `character` vector of files to read.
`metadata`	A `character` path and filename of a CSV file containing additional metadata about the samples
`header.size`	A `numeric` indicating the number of lines in the header (default 2)
`skip`	`numeric` how many lines to skip before reading (default 8)
`cycle.threshold`	The maximum number of PCR cycles performed (default 40) `numeric`
`metadataColClasses`	Optional `character` vector giving the column classes of the metadata file. See read.table.
`meta.key`	Optional `character` vector that identifies the key column between the metadata and the fluidigm data
`idvars`	Optional `character` vector that defines the set of columns uniquely identifying a well (unique cell, gene, and condition).
`splitby`	Optional `character` that defines the column / variable used to split the resulting data into a list of SingleCellAssay, such that unique levels of `splitby` each fall into their own SingleCellAssay. Ususally the experimental unit subjected to different treatments.
`unique.well.id`	The column that uniquely identifies a sample well in the data. Default is "Chamber.ID".
`raw`	`logical` flag indicating this is raw data coming off the instrument. Thus we make some assumptions about the column names that are present.
`assay`	`character` name of a column that uniquely identifies an Assay (i.e. gene). Default is NULL
`geneid`	`character` names of the column that identifies a gene. Default is "Assay.Name"
`sample`	`character` name of a column that uniquely identifies a sample
`well`	`character` name of a column that uniquely identifies a well. Default "Well".
`measurement`	`character` name of the column that holds the measurement. Default "X40.Ct".
`measurement.processed`	`character` one of "Ct","40-Ct", or "et". If not "Ct", the measurement will be transformed.
`ncells`	The column with the number of cells in this well.