readCodelink {codelink}R Documentation

Read Codelink Bioarrays Data

Description

Read data exported as text by Codelink Software. It reads values (normalized by Codelink Software or not) flags and information about probes.

Usage

    readCodelink(files=list.files(pattern="TXT"), sample.name=NULL,
        flag, dec=NULL, type="Spot",    preserve=FALSE, verbose=2,
        file.type="Codelink", check=TRUE, fix=FALSE)

Arguments

files list of files to read.
sample.name vector of same length as files with sample names.
flag list with values to assign based on Flag quality values.
dec character indicating the decimal character used in the files.
type character indicating which base value to read from files.
preserve logical, if TRUE Bkgd_stdev slot is not removed (if present).
verbose numerical, set the level of information. Level 2 set as old behaviour. Level > 2 output some debug info.
file.type exported file type, currently Codelink or XLS file formats supported.
check logical, check for probe order consistency.
fix logical, try to fix probe order consistency.

Details

Value

An object of class "Codelink".

Note

Author(s)

Diego Diez

See Also

read.table

Examples

## Not run: 
    # reading default extension (TXT).
    data <- readCodelink()

    # specify a different one.
    files <- list.files(pattern = "txt")
    data <- readCodelink(files = files)

    # example.
    data(codelink.example)
## End(Not run)

[Package codelink version 1.6.0 Index]