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:
uniquepep
is set to TRUE (default), only unique
proteotypic identification and quantitation peptides are retained.fdr(default is 0.01)
using the "BH" method (seefdr
andfdrMethod
parameters for details).=
quantppm
andidentppm
) are filtered out.fpr
are filtered out.loess
function for thestats
package) using
a defaultspan
value of 0.05.grid.nsd.from
,grid.nsd.to
andgrid.nsd.by
parameters) and from 2 to 20 by 2 parts per
million (ppm) for mass tolerance (seegrid.ppm.from
,grid.ppm.to
andgrid.ppm.by
parameters).
The data can be subset using using an absolute number of features
(seegrid.n
) or a fixed percentage (seegrid.subset
).
The pair of optimalnsd
andppm
is chosen
(seegrid.param.sel
parameter).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 browser
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