globalQuality {arrayQuality} | R Documentation |
This function provides Quality Control measures for GenePix, Spot and Agilent format files. It is used to create a table of measures to be used as reference in gpQuality, spotQuality or agQuality.
globalQuality(fnames = NULL, path = ".", organism = c("Mm", "Hs"), output = FALSE, resdir = ".", DEBUG = FALSE, inputsource = "readGPR",...)
fnames |
A "character" string naming the input files. |
path |
a "character" string representing the data directory. By default this is set to the current working directory ("."). |
organism |
A "character" string naming the organism genome printed on the array, either "Mm" or "Hs". By default, organism is set to "Mm". It is used to retrieve the corresponding reference tables. |
output |
Logical. If 'TRUE', the quality measures are printed to a file. |
resdir |
A "character" string representing the directory where the results will be saved. By default, this is set to the current working directory ("."). |
DEBUG |
If 'TRUE', debug statements are printed. |
inputsource |
A "character" string providing the name of the function to use to read the input files. It should be inputsource = "readGPR" for GenePix format files, inputsource = "readSpot" for Spot files, or inputsource = "readAgilent" for Agilent format. By default, 'inputsource' is set to "readGPR". |
... |
additional arguments |
A matrix of Quality Control measures, each column representing a different input slide.
Agnes Paquet
gpQuality
, slideQuality
,
MmReferenceDB
, readGPR
,
readSpot
, readAgilent
datadir <- system.file("gprQCData", package="arrayQuality") if (interactive()) reference <- globalQuality(fnames="9Mm137.gpr", path=datadir, organism="Mm")