PRv9mers: Print Run Quality version 9mers

In arrayQuality: Assessing array quality on spotted arrays

Description

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

Usage

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

Arguments

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

Details

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).

Value

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

Author(s)

Jean Yee Hwa Yang

Examples

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

arrayQuality documentation built on Nov. 8, 2020, 5:12 p.m.