bioconductor v3.9.0 Affyio
Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.
Link to this section Summary
Functions
CDF file format function
Extract Dates from CEL files
Internal affyio functions
Read CDF file into an R list
Read a CEL file into an R list
Read header information from cel file
Read PM or MM from CEL file into matrices
Link to this section Functions
checkcdftype()
CDF file format function
Description
This function returns a text string giving the file format for the supplied filename
Usage
check.cdf.type(filename)Arguments
| Argument | Description |
|---|---|
filename | fullpath to a cdf file |
Value
Returns a string which is currently one of:
*
Author
B. M. Bolstad bmb@bmbolstad.com
getcelfiledates()
Extract Dates from CEL files
Description
This function reads the header information for a series of CEL files then extracts and returns the dates.
Usage
get.celfile.dates(filenames, ...)Arguments
| Argument | Description |
|---|---|
filenames | a vector of characters with the CEL filenames. May be fully pathed. |
list() | further arguments passed on to read.celfile.header . |
Details
The function uses read.celfile.header to read in the header of each file. The ScanDate component is then parsed to extract the date.
Note that an assumption is made about the format. Namely, that dates are in the Y-m-d or m/d/y format.
Value
A vector of class Date with one date for each celfile.
Seealso
See Also as read.celfile.header .
Author
Rafael A. Irizarry rafa@jimmy.harvard.edu
read_abatch()
Internal affyio functions
Description
Internal affyio functions
Details
These are not to be called directly by a user. They support the affy package
readcdffilelist()
Read CDF file into an R list
Description
This function reads the entire contents of a cdf file into an R list structure
Usage
read.cdffile.list(filename, cdf.path = getwd())Arguments
| Argument | Description |
|---|---|
filename | name of CDF file |
cdf.path | path to cdf file |
Details
Note that this function can be very memory intensive with large CDF files.
Value
returns a list structure. The exact contents may vary
depending on the file format of the cdf file (see check.cdf.type )
Author
B. M. Bolstad bmb@bmbolstad.com
readcelfile()
Read a CEL file into an R list
Description
This function reads the entire contents of a CEL file into an R list structure
Usage
read.celfile(filename,intensity.means.only=FALSE)Arguments
| Argument | Description |
|---|---|
filename | name of CEL file |
intensity.means.only | If TRUE then read on only the MEAN section in INTENSITY |
Details
The list has four main items. HEADER, INTENSITY, MASKS, OUTLIERS. Note that INTENSITY is a list of three vectors MEAN, STDEV, NPIXELS. HEADER is also a list. Both of MASKS and OUTLIERS are matrices.
Value
returns a list structure. The exact contents may vary
depending on the file format of the CEL file
Author
B. M. Bolstad bmb@bmbolstad.com
readcelfileheader()
Read header information from cel file
Description
This function reads some of the header information (appears before probe intensity data) from the supplied cel file.
Usage
read.celfile.header(filename,info=c("basic","full"),verbose=FALSE)Arguments
| Argument | Description |
|---|---|
filename | name of CEL file. May be fully pathed |
info | A string. basic returns the dimensions of the chip and the name of the CDF file used when the CEL file was produced. full returns more information in greater detail. |
verbose | a logical . When true the parsing routine prints more information, typically useful for debugging. |
Value
A list data structure.
Author
B. M. Bolstad bmb@bmbolstad.com
readcelfileprobeintensitymatrices()
Read PM or MM from CEL file into matrices
Description
This function reads PM, MM or both types of intensities into matrices. These matrices have all the probes for a probeset in adjacent rows
Usage
read.celfile.probeintensity.matrices(filenames, cdfInfo, rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE, verbose=FALSE, which= c("pm","mm","both"))Arguments
| Argument | Description |
|---|---|
filenames | a character vector of filenames |
cdfInfo | a list with items giving PM and MM locations for desired probesets. In same structure as returned by make.cdf.package |
rm.mask | a logical . Return these probes as NA if there are in the [MASK] section of the CEL file |
rm.outliers | a logical . Return these probes as NA if there are in the [OUTLIERS] section of the CEL file |
rm.extra | a logical . Return these probes as NA if there are in the [OUTLIERS] section of the CEL file |
verbose | a logical . When true the parsing routine prints more information, typically useful for debugging. |
which | a string specifing which probe type to return |
Value
returns a list of matrix items. One
matrix contains PM probe intensities, with probes in rows and arrays
in columns
Author
B. M. Bolstad bmb@bmbolstad.com