PRv9mers {arrayQuality}R Documentation

Print Run Quality version 9mers


Qualitative diagnostic plots looking at print-run quality. This component examine the 9mers hybridizations.


PRv9mers(fnames, path = ".", dev = "png", DEBUG = FALSE, prargs = NULL, samepr = TRUE, prname = "xMm", save = TRUE, ...)


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 (".").
dev A "character" string naming the graphics device. This will take arguments "png", "jpeg" and "ps" only.
DEBUG If 'TRUE', debug statements are printed.
prargs A list with 4 components: Block, Row, Column and ncolumns. See Details for more information.
samepr If 'TRUE', we assume everything in the directory are from the same print-run.
prname A "character" string giving the name of the print-run.
save If `TRUE', the figures will be saved to files.
... additional arguments


The argument "prargs" is used to calculate the layout information about a print-run. Components Block, Row and Columns denote the column names from the input data representing the print-tip location. The component "ncolumns" is an integer representing the number of print-tip columns in the data. If the arguement is set to NULL, the the following default will be used. list(Block="Block", Row="Row", Column="Column", ncolumns=4)


Files of diagnostic plots and excel files containings probe IDs of problematic probes.


Jean Yee Hwa Yang


datadir <- system.file("gprQCData", package="arrayQuality")
if (interactive())
PRv9mers(fnames="12Mm250.gpr", path=datadir, prname="12Mm")

[Package arrayQuality version 1.0.7 Index]