marrayTools {marray} | R Documentation |
This functions will produce a directory of diagnostic plots, quality measures and normalization.
spotTools(fnames, path = ".", galfile, bg = TRUE, plot = TRUE, quality = TRUE, fill = TURE, raw = FALSE, echo = TRUE, ...) gpTools(fnames, path = ".", galfile, bg = TRUE, plot = TRUE, quality = TRUE, fill = TRUE, raw = FALSE, echo = TRUE, ...)
fnames |
a vector of character strings containing the file names of
each spot quantification data file. These typically end in .spot
for the software Spot or .gpr for the software GenePix . |
path |
a character string representing the data directory. By
default this is set to the current working directory ("."). In the
case where fnames contains the full path name, path should be set
to NULL. |
galfile |
a character string representing the Gal file. |
bg |
logical: if 'TRUE', background correction is performed before normalization |
plot |
logical: if 'TRUE', maDiagnPlots is call to generate basic diagnostic plot per array. |
quality |
logical: if 'TRUE', maQuality is call to calculate basic quality measures. |
fill |
logical: if `TRUE', `scan' will implicitly add empty fields to any lines with fewer fields than implied by `what'. |
raw |
logical: if 'TRUE', the microarray object class of 'marrayRaw' is return rather than 'marrayNorm'. |
echo |
logical: if 'TRUE' (default), run-time information of the array currently being process is printed. |
... |
further arguments to scan or maNorm . |
Jpeg files of diagnostic plots, excel files of quality measures, tab
delimited files of normalized log-ratios and log-intensities values are
saved to disk.
In addition, an object of class marrayRaw
or marrayNorm
is return.
Yee Hwa (Jean) Yang
data(swirl) datadir <- system.file("swirldata", package="marray") ## normdata <- spotTools(path=datadir, quality=FALSE)