read.fluidigm {MAST} | R Documentation |
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 |
metadata |
A |
header.size |
A |
skip |
|
cycle.threshold |
The maximum number of PCR cycles performed (default 40) |
metadataColClasses |
Optional |
meta.key |
Optional |
idvars |
Optional |
splitby |
Optional |
unique.well.id |
The column that uniquely identifies a sample well in the data. Default is "Chamber.ID". |
raw |
|
assay |
|
geneid |
|
sample |
|
well |
|
measurement |
|
measurement.processed |
|
ncells |
The column with the number of cells in this well. |
list of SingleCellAssay
holding the data.
Greg Finak