Description Usage Arguments Details Value Objects from the Class Slots Methods Author(s) See Also Examples
The RPPASet class fits supercurves to an entire directory of reverse-phase protein array experiments.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | RPPASet(path,
designparams,
fitparams,
spatialparams=NULL,
normparams,
doprefitqc=FALSE,
monitor=SCProgressMonitor(),
antibodyfile=NULL,
software="microvigene",
alt.layout=NULL)
is.RPPASet(x)
## S4 method for signature 'RPPASet'
normalize(object,
...)
## S4 method for signature 'RPPASet'
summary(object,
onlynormqcgood=ran.prefitqc(object),
...)
## S4 method for signature 'RPPASet'
write.summary(object,
path,
prefix="supercurve",
graphs=TRUE,
tiffdir=NULL,
onlynormqcgood=ran.prefitqc(object),
monitor=NULL,
...)
|
path |
character string specifying a directory. In the case of
the |
designparams |
object of class |
fitparams |
object of class |
spatialparams |
object of class |
normparams |
object of class |
doprefitqc |
logical scalar. If |
monitor |
object of (sub)class |
antibodyfile |
character string specifying filename containing mapping from quantification files to antibodies |
software |
character string specifying the software used to generate
the quantification file (see section ‘Details’ of
|
alt.layout |
character string specifying the name of the alternative
layout to be used (see section ‘Details’ of |
object |
object of class |
prefix |
character string used as a filename prefix on files generated by the write.summary method. |
graphs |
logical scalar. If |
tiffdir |
character string specifying the directory containing the TIFF images corresponding to the quantification files |
onlynormqcgood |
logical scalar. If |
x |
object of class |
... |
extra arguments for generic or plotting routines |
Quantify all the slides in a directory using RPPASet
generator.
This returns an object containing slide data and fits for each slide.
Typically this is followed by a call to write.summary
to write
the resulting quantifications and diagnostic plots to a directory.
The write.summary
method (indirectly) generates three CSV
files: one for the raw concentrations, one for the R^2 statistics,
and one for the normalized concentrations.
If tiffdir
is NULL
, the directory is assumed to be a sibling
directory to path
named "tif". If graphs
is TRUE
,
two PNG files containing output graphs are created per antibody.
The ImageMagick ‘convert’ binary is then used to merge these output
graphs with the source TIFF files, generating an additional
JPEG file per antibody.
The RPPASet
generator returns an object of class RPPASet
.
The is.RPPASet
method returns TRUE
if its
argument is an object of class RPPASet
.
The summary
method returns an object of class RPPASetSummary
.
The write.summary
method invisibly returns NULL
.
Although objects of the class can (in theory) be created by a direct call
to new, the only realistic method is to use the
RPPASet
generator function.
call
:object of class call
specifying the function
call that was used during construction
version
:character string containing the version of this package used to construct the object
design
:object of class RPPADesign
, common to all
the slides
rppas
:array of objects of class RPPA
spatialparams
object of class RPPASpatialParams
that was used to perform spatial adjustment, or NULL
prefitqcs
:array of objects of class
RPPAPreFitQCParams
fitparams
:object of class RPPAFitParams
that was
used to construct the model fits
normparams
:object of class RPPANormalizationParams
used to normalize the raw concentrations
fits
:array of fitted objects of class RPPAFit
completed
:logical matrix specifying stage completion for each slide
signature(object = "RPPASet")
:
Assembles matrix of concentrations from all fits in object,
using the object's normalization settings.
signature(object = "RPPASet")
:
Creates an object of class RPPASetSummary
.
signature(object = "RPPASet")
:
Writes a record of the entire RPPASet, including fitted values,
residuals, and images of the processed slides.
Kevin R. Coombes kcoombes@mdanderson.org, P. Roebuck proebuck@mdanderson.org
RPPA
,
RPPADesign
,
RPPAFit
,
RPPASetSummary
,
SCProgressMonitor
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | ## Not run:
parentdir <- file.path("C:", "MyData")
txtdir <- file.path(parentdir, "txt") # quantification files
imgdir <- file.path(parentdir, "tif") # and corresponding image files
outdir <- file.path(parentdir, "results") # output files
designparams <- RPPADesignParams(grouping="blockSample",
center=FALSE,
aliasfile="layoutInfo.tsv",
designfile="slidedesign.tsv")
fitparams <- RPPAFitParams(measure="Mean.Net",
method="nlrob",
model="cobs",
ignoreNegative=FALSE,
warnLevel=-1,
verbose=FALSE)
normparams <- RPPANormalizationParams(method="vs")
monitor <- SCProgressMonitor()
rppaset <- RPPASet(txtdir,
designparams,
fitparams,
normparams=normparams,
monitor=monitor)
write.summary(rppaset,
path=outdir,
graphs=TRUE,
tiffdir=imgdir,
monitor=monitor)
## End(Not run)
|
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