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")
character
vector of files to read.character
path and filename of a CSV file containing additional metadata about the samplesnumeric
indicating the number of lines in the header (default 2)numeric
how many lines to skip before reading (default 8)numeric
character
vector giving the column classes of the metadata file. See read.table.character
vector that identifies the key column between the metadata and the fluidigm datacharacter
vector that defines the set of columns uniquely identifying a well (unique cell, gene, and condition).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.logical
flag indicating this is raw data coming off the instrument. Thus we make some assumptions about the column names that are present.character
name of a column that uniquely identifies an Assay (i.e. gene). Default is NULLcharacter
names of the column that identifies a gene. Default is "Assay.Name"character
name of a column that uniquely identifies a samplecharacter
name of a column that uniquely identifies a well. Default "Well".character
name of the column that holds the measurement. Default "X40.Ct".character
one of "Ct","40-Ct", or "et". If not "Ct", the measurement will be transformed.list of SingleCellAssay
holding the data.