PRv9mers {arrayQuality} | R Documentation |
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 argument 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")