read.cel.complete {affxparser} | R Documentation

## Parsing an Affymetrix CEL file

### Description

Parsing an Affymetrix CEL file using the Fusion SDK. The intention is to let users obtain all (but possibly a subset of) information in the CEL file.

### Usage

    read.cel.complete(fname, indices = NULL, read.intensities = TRUE,
                      read.stdvs = TRUE, read.pixels = TRUE,
                      read.xy = FALSE, read.outliers = TRUE,
                      read.masked = TRUE, verbose = 0)

### Arguments

`fname` | the name of the CEL file.
`indices` | a vector of indices indicating which features to read. If the argument is `NULL` all features will be returned.
`read.intensities` | a logical: will the intensities be returned.
`read.stdvs` | a logical: will the standard deviations be returned.
`read.pixels` | a logical: will the number of pixels be returned.
`read.xy` | a logical: will the (x,y) coordinates be returned.
`read.outliers` | a logical: will the outliers be return.
`read.masked` | a logical: will the masked features be returned.
`verbose` | how verbose do we want to be. 0 is no verbosity, higher numbers mean more verbose output. At the moment the values 1 and 2 are supported.

### Details

This function reads everything from a CEL file. It is considered a bug if the file contains information not accessible by this function, please report it.

The (input and output) interface makes heavily use of the concept of indices. An (x,y) coordinate is converted to an integer by the formula (y + 1) times numberOfColsInCelFile + (x + 1), assuming that the (x,y) coordinates start at (0,0).

The file returns a list with components (possible empty depending on the input flags) corresponding to the various flags. The `outliers` and `masked` components are special in that they are vectors of indices of features flagged as respectively outlier/masked by the Affymetrix image software.

### Value

A named list with components described below. The order of the `intensities`, `stdvs` and `pixels` corresponds to the ordering of the `indices` argument.

`header` | The header of the CEL file. Equivalent to the output from `read.cel.header`, see the documentation for that function.
`intensities` | A vector of mode `nummeric` containing the intensity associated with each feature, unless `read.intensities = FALSE` in which case it will be `NULL`. Restricted to features within the `indices` range.
`stdvs` | A vector of mode `nummeric` containing the standard deviation associated with each feature, unless `read.stdvs = FALSE` in which case it will be `NULL`. Restricted to features within the `indices` range.
`pixels` | A vector of mode `integer` containing the number of pixels associated with each feature, unless `read.pixels = FALSE` in which case it will be `NULL`. Restricted to features within the `indices` range.
`x` | A vector of mode `integer` containing the x coordinate associated with each feature, unless `read.xy = FALSE` in which case it will be `NULL`. Restricted to features with the `indices` range.
`y` | A vector of mode `integer` containing the y coordinate associated with each feature, unless `read.xy = FALSE` in which case it will be `NULL`. Restricted to features with the `indices` range.
`outliers` | A vector of mode `integer` which the indices of the features flagged as outliers, unless `read.outliers = NULL` in which case it will be `NULL`. Note that there is a difference between `outliers = NULL` and `outliers = integer(0)` - the last case happens when `read.outliers = TRUE` but there are no outliers. In case an `indices` argument is given, only indices within the `indices` argument are returned.
`masked` | A vector of mode `integer` which the indices of the features flagged as masked, unless `read.masked = NULL` in which case it will be `NULL`. Note that there is a difference between `masked = NULL` and `masked = integer(0)` - the last case happens when `read.masked = TRUE` but there are no masked features. In case an `indices` argument is given, only indices within the `indices` argument are returned.

### Note

Memory usage: the Fusion SDK allocates memory for the entire CEL file, when the file is accessed (but does not actually read the file into memory). Using the `indices` argument will therefore only affect the memory use of the final object (as well as speed), not the memory allocated in the C function used to parse the file. This should be a minor problem however.

The outlier/masked flag are computed by the Affymetrix image analysis software. The current community view seems to be that this should be done based on statistical modelling of the actual probe intensities and should be based on the choice of preprocessing algorithm. Mopst algorithms are only using the intensities from the CEL file.

### Author(s)

James Bullard, bullard@stat.berkeley.edu and Kasper Daniel Hansen, khansen@stat.berkeley.edu

### See Also

`affxparserInfo` for a package overview and `read.cel.header` for a description of the header output. Often a user only wants to read the intensities, look at `read.cel.intensities` for a function specialized for that use. See `xy2indices` from affy and `xy2i` from makePlatformDesign for a discussion of the index approach.

### Examples

    ## Not run:
    read.cel.complete("~/testFile.CEL", read.npixels = FALSE)
    ## End(Not run)

[Package affxparser version 1.2.0 Index]