runPDTMTptmAnalysis.RdLaunch an analysis workflow to detect post-translational modifications
based on outputs from separate protein- and peptide-level analyses run
with runPDTMTAnalysis().
runPDTMTptmAnalysis(
templateRmd = system.file("extdata/process_PD_TMT_PTM_template.Rmd", package =
"einprot"),
outputDir = ".",
outputBaseName = "PDTMTptmAnalysis",
reportTitle = "PD/PTM data processing",
reportAuthor = "",
forceOverwrite = FALSE,
experimentInfo = list(),
species,
sceProteins,
scePeptides,
assayForTests,
assayImputation,
idCol,
labelCol,
proteinIdColProteins = function(df) einprot::getFirstId(df, "einprotProtein", ";"),
proteinIdColPeptides = function(df) einprot::getFirstId(df, "einprotProtein", ";"),
comparisons = list(),
ctrlGroup = "",
allPairwiseComparisons = TRUE,
singleFit = TRUE,
subtractBaseline = FALSE,
baselineGroup = "",
testType = "interaction",
minNbrValidValues = 2,
minlFC = 0,
volcanoAdjPvalThr = 0.05,
volcanoLog2FCThr = 1,
volcanoMaxFeatures = 25,
volcanoLabelSign = "both",
volcanoFeaturesToLabel = "",
addInteractiveVolcanos = FALSE,
interactiveDisplayColumns = NULL,
interactiveGroupColumn = NULL,
seed = 42,
linkTableColumns = c(),
customYml = NULL,
doRender = TRUE
)Path to the template R Markdown file. Typically does not need to be modified.
Path to a directory where all output files will be written. Will be created if it doesn't exist.
Character string providing the 'base name' of the output files. All output files will start with this prefix.
Character scalars, giving the title and author for the result report.
Logical, whether to force overwrite an existing
Rmd file with the same outputBaseName in the outputDir.
Named list with information about the experiment. Each entry of the list must be a scalar value.
Character scalar providing the species. Must be one of the
supported species (see getSupportedSpecies()). Either the common
or the scientific name can be used.
Character strings pointing to .rds files with
SingleCellExperiment objects containing proteins and
peptides, respectively and generated by runPDTMTAnalysis().
File paths will be expressed in canonical form (using
normalizePath()) before they are processed.
Character string giving the name of the assay to use for testing.
Character string giving the name of the assay containing information about the imputation status of each observation.
Arguments defining the feature identifiers (row names,
should be unique) and feature labels (for plots, can be anything).
Each of these arguments can be either a character vector of column
names in the input file (after application of make.names),
in which case the corresponding feature ID
is generated by simply concatenating the values in these columns, or a
function with one input argument (a data.frame, corresponding to the
annotation columns of the input file), returning a
character vector corresponding to the desired feature IDs.
Character strings pointing
to columns of the rowData of the respective objects that
contain the protein identifiers (will be used to match the two objects).
List of character vectors defining comparisons to
perform. The first element of each vector represents the
denominator of the comparison. If not empty, ctrlGroup and
allPairwiseComparisons are ignored.
Character vector defining the sample group(s) to use as control group in comparisons.
Logical, should all pairwise comparisons be performed?
Logical scalar indicating whether a single model fit
should be used (and results for pairwise comparisons extracted via
contrasts). If FALSE, the data set will be subset to the
relevant samples for each comparison. Only applicable if
testType is "interaction".
Logical scalar, whether to subtract the background/
reference value for each feature in each batch before fitting the
model. If TRUE, requires that a 'batch' column is available.
Character scalar representing the reference group.
Only used if subtractBaseline is TRUE, in which case the
abundance values for a given sample will be adjusted by subtracting the
average value across all samples in the baselineGroup from the
same batch as the original sample.
The testing approach to use, either "interaction"
or "welch" (similar to the approach used by MSstatsPTM).
Numeric, the minimum number of valid values (must be met in both the protein and peptide objects) for a peptide to be used for statistical testing.
Numeric, minimum log fold change to test against (only used
if testType = "interaction").
Numeric, adjusted p-value threshold to determine which proteins to highlight in the volcano plots.
Numeric, log-fold change threshold to determine which proteins to highlight in the volcano plots.
Numeric, maximum number of significant features to label in the volcano plots.
Character scalar, either 'both', 'pos', or 'neg', indicating whether to label the most significant features regardless of sign, or only those with positive/negative log-fold changes.
Character vector with features to always label in the volcano plots (regardless of significance).
Logical scalar indicating whether to add
interactive volcano plots to the html report. For experiments with
many quantified features or many comparisons, setting this to
TRUE can make the html report very large and difficult to
interact with.
Character vector (or NULL)
indicating which columns to include in the tooltip for the
interactive volcano plots. The default shows the feature ID.
Character scalar (or NULL, default)
indicating the column to group points by in the interactive volcano
plot. Hovering over a point will highlight all other points with the
same value of this column.
Numeric, random seed to use for any non-deterministic calculations.
Character vector with regular expressions that will be matched against the column names of the rowData of the generated SingleCellExperiment object and included in the link table in the end of the report.
Character string providing the path to a custom YAML file
that can be used to overwrite default settings in the report. If set
to NULL (default), no alterations are made.
Logical scalar. If FALSE, the Rmd file will be
generated (and any parameters injected), but not rendered.
Invisibly, the path to the compiled html report.