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.