readAgilent: Read Agilent .txt files
In seandavi/Rpressa: A collection of useful code for bioinformatics

Description Usage Arguments Value Author(s) See Also

This is a fairly smart function for reading Agilent text files for miRNA, CGH, and one- and two-color expression arrays.

readAgilent(fnames,
            path,
            dataColumns = NULL,
            annotationColumns = NULL,
            source = c("mirna", "cgh", "onecolorexpression",
                       "twocolorexpression"),
            exprs = 1, ...)

`fnames`	A character() vector of file names
`path`	The base file path for the associated file names.
`dataColumns`	The column names of the data columns to be included. A single matrix will be included in the assayData of the resulting `AgilentSet` object for each data column named here. Based on the source parameter, logical defaults are defined if this is NULL.
`annotationColumns`	The column names of the annotation columns to be read. These columns will be read from the first file and included in the featureData of the resulting `AgilentSet` object. Based on the source parameter, logical defaults are defined if this is NULL.
`source`	A single character string describing the type of array. This selection defines the defaults for annotationColumns and dataColumns.
`exprs`	The integer index of the dataColumns vector to be assigned to the exprs() slot in the resulting `AgilentSet`.
`...`	Passed to read.table.