'character' string, or a vector of character string specifying the name of the file(s) to read in
path
'character' string specifying the location of file to be read by the function
cdfName
'character' defining the chip annotation (manifest) to use
('human370v1c', human550v3b', 'human650v3a', 'human1mv1c',
'human370quadv3c', 'human610quadv1b', 'human660quadv1a',
'human1mduov3b', 'humanomni1quadv1b', 'humanomniexpress12v1b', 'humancytosnp12v2p1h')
colnames
list containing elements 'SampleID', 'SNPID', 'XRaw' and 'YRaw', which specify the column names from
in 'file' that pertain to these variables. The default should suffice in most situations.
type
list containing data types for the columns to be read in. The default should be fine in most situations.
verbose
'logical'. Should processing information be displayed as data is read in?
Details
This function returns an NChannelSet containing raw intensity data (X and Y) from GenCall final report file.
It assumes the GenCall output is formatted to have samples listed one below the other, and that the columns 'X Raw' and 'Y Raw' are available in the file.
The function crlmmillumina() can be run on the output of the readGenCallOutput function.