Reads a Fluidigm Biomark (c. 2011) raw data file (or set of files)

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"
)

Arguments

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.

Value

list of SingleCellAssay holding the data.

Author

Greg Finak