read.fluidigm {MAST} | R Documentation

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

### Description

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.

### Usage

    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(s)

Greg Finak

[Package MAST version 1.10.0 Index]