Reads a fluidigm raw data file (or set of files)
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")A character vector of files to read.
A character path and filename of a CSV file containing additional metadata about the samples
A numeric indicating the number of lines in the header (default 2)
numeric how many lines to skip before reading (default 8)
The maximum number of PCR cycles performed (default 40) numeric
Optional character vector giving the column classes of the metadata file. See read.table.
Optional character vector that identifies the key column between the metadata and the fluidigm data
Optional character vector that defines the set of columns uniquely identifying a well (unique cell, gene, and condition).
Optional character that defines the column / variable used to split the resulting data into an SCASet, such that unique levels of splitby each fall into their own SingleCellAssay object within an SCASet. Ususally the experimental unit subjected to different treatments.
The column that uniquely identifies a sample well in the data. Default is "Chamber.ID".
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 NULL
character names of the column that identifies a gene. Default is "Assay.Name"
character name of a column that uniquely identifies a sample
character 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.
The column with the number of cells in this well.
SCASet holding the data.
This function reads a raw Fluidigm data file or set of files and constructs a SingleCellAssay (or FluigidmAssay) object.