filenames, creates a complete html report and
saves/exports all results as csv and rda files.
See details for a description of the pipeline and
Synapter for manual execution of individual steps.synergise(filenames, master = FALSE, object, outputdir, fdr = 0.01,
fdrMethod = c("BH", "Bonferroni", "qval"), fpr = 0.01, peplen = 7,
missedCleavages = 0, identppm = 20, quantppm = 20, uniquepep = TRUE,
span = 0.05, grid.ppm.from = 2, grid.ppm.to = 20, grid.ppm.by = 2,
grid.nsd.from = 0.5, grid.nsd.to = 5, grid.nsd.by = 0.5,
grid.subset = 1, grid.n = 0, grid.param.sel = c("auto", "model",
"total", "details"), mergedEMRTs = c("rescue", "copy", "transfer"),
css = NULL, verbose = TRUE)list of file names to be load. The
names must be identpeptide, quantpeptide,
quantpep3d and fasta. If missing, a dialog box opens
to select files interactively. identpeptide can be a csv
final peptide file (from PLGS) or a saved "MasterPeptides "
data object as created by makeMaster if working with
master peptide data. To serialise the "MasterPeptides "
instance, use the saveRDS function, and file extenstion rds.logical indicating if the identification final
peptide files are master (see makeMaster) or
regular files. Default is FALSE.Synapter that will be
copied, processed and returned. If filenames are also
provided, the latter and object's inputFiles will be
checked for equality.character with the full path to an
existing directory."BH"
(default) for Benjamini and HochBerg (1995), "Bonferroni"
for Bonferroni's single-step adjusted p-values for strong control
of the FWER and "qval" from the qvalue package. See
Synapter for references.logical is length 1 indicating if only
unique peptides in the identification and quantitation peptides as
well as unique tryptic peptides as defined in the fasta
file. Default is TRUE.auto (default), details, model or
total. See Synapter for details on these
selection methods."rescue" (default), "copy"
or "transfer". See the documentation for the
findEMRTs function in Synapter for details.NULL
(default), uses synapter.css.logical indicating if progress output
should be printed to the console. Default is TRUE.Synapter.
Used for its side effect of creating an html report of
the run in outputdir.Synapter object if available or
as a list of files (see filenames) that will be used to read the
data in. If none of object and filenames are provided, file
section menus are open to select input files. The html report and result
files will be created in the outputdir folder. If not provided,
the destination can be selected through a selection menu. All other
input parameters have default values.The data processing and analysis pipeline is as follows:
uniquepepis set to TRUE (default), only unique
proteotypic identification and quantitation peptides are retained.fdr(default is 0.01)
using the "BH" method (seefdrandfdrMethodparameters for details).quantppmandidentppm) are filtered out.fprare filtered out.loessfunction for thestatspackage) using
a defaultspanvalue of 0.05.grid.nsd.from,grid.nsd.toandgrid.nsd.byparameters) and from 2 to 20 by 2 parts per
million (ppm) for mass tolerance (seegrid.ppm.from,grid.ppm.toandgrid.ppm.byparameters).
The data can be subset using using an absolute number of features
(seegrid.n) or a fixed percentage (seegrid.subset).
The pair of optimalnsdandppmis chosen
(seegrid.param.selparameter).master is set to TRUE, default
is FALSE), the relevant actions that have already been executed when
the file was created with makeMaster are not repeated here.output <- tempdir() ## a temporary directory
synapterTinyData()
synergise(object = synapterTiny, outputdir = output, grid.subset = 0.2)
htmlReport <- paste0("file:///", file.path(output, "index.html")) ## the result report
browseURL(htmlReport) ## open the report with default browserRun the code above in your browser using DataLab