registerDEFields {iSEEu} | R Documentation |
Register the names of fields containing various DE statistics, to populate the user interface of DE-related Panels.
registerPValueFields(se, fields) registerAveAbFields(se, fields) registerLogFCFields(se, fields) registerPValuePatterns(se, patterns) registerAveAbPatterns(se, patterns) registerLogFCPatterns(se, patterns) getPValueFields(se) getAveAbFields(se) getLogFCFields(se) getPValuePatterns(se, defaults = c("PValue", "p.value", "pval")) getAveAbPatterns(se, defaults = c("AveExpr", "logCPM")) getLogFCPatterns(se, defaults = c("logFC", "LogFC"))
se |
A SummarizedExperiment to be visualized with various DE-related Panels.
This is expected to have a number of DE-related fields in its |
fields |
A character vector containing the names of the relevant fields containing the DE statistics.
Alternatively |
patterns |
A character vector containing partial names,
to match against the |
defaults |
Character vector specifying the default patterns to provide when no patterns were registered in |
DE-related Panels need to find relevant rowData
fields containing p-values, log-fold changes, etc. to set appropriate defaults in the user interface.
These functions allow a user to tune the definition of what those Panels consider to be relevant,
which is occasionally necessary if the DE statistics are stored in a rowData
field with an unusual column name.
The idea is to register
the relevant fields in se
, which can then be supplied to iSEE
with the affected Panels - see Examples.
The registered fields
should be the names of appropriate columns in rowData
containing continuous variables.
Columns containing categorical or non-atomic variables will generally be ignored.
For each DE statistic, if any fields
are registered in se
, they will be used directly and patterns
will be ignored.
The registered patterns
are used for partial name matching to the names of appropriate columns of rowData
.
All partial matching must be exact - regular expressions are not supported.
Matches can occur anywhere in the name.
For example, with "PValue"
, columns with the names "PValue.X"
and "X.PValue"
will be considered acceptable matches.
If no patterns
are supplied, the Panels will use the values in defaults
.
All register
functions will return se
, modified to contain the supplied patterns
or fields
.
These will be used as suggestions by DE-related Panels to identify the relevant fields.
All get
functions will return a character vector containing the value set by the corresponding register
function;
or NULL
, if nothing was set.
Aaron Lun
# Making up some results with unusual names. se <- SummarizedExperiment(matrix(rnorm(10000), 1000, 10)) rownames(se) <- paste0("GENE_", seq_len(nrow(se))) rowData(se)$pvalue <- runif(nrow(se)) rowData(se)$lfc <- rnorm(nrow(se)) rowData(se)$average <- rnorm(nrow(se)) se <- registerPValueFields(se, "pvalue") getPValueFields(se) se <- registerAveAbFields(se, "average") getAveAbFields(se) se <- registerLogFCFields(se, "lfc") getLogFCFields(se) if (interactive()) { iSEE(se, initial=list(MAPlot())) }