Register DE-related fields

Register the names of fields containing various DE statistics, to populate the user interface of DE-related Panels.

Usage

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"))

Arguments

se

A SummarizedExperiment to be visualized with various DE-related Panels. This is expected to have a number of DE-related fields in its rowData.

fields

A character vector containing the names of the relevant fields containing the DE statistics. Alternatively NULL to remove any existing setting.

patterns

A character vector containing partial names, to match against the colnames of the rowData to identify relevant fields containing DE statistics. Alternatively NULL to remove any existing setting.

defaults

Character vector specifying the default patterns to provide when no patterns were registered in se.

Value

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.

Details

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.

Author

Aaron Lun

Examples

# 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)
#> [1] "pvalue"
se <- registerAveAbFields(se, "average")
getAveAbFields(se)
#> [1] "average"
se <- registerLogFCFields(se, "lfc")
getLogFCFields(se)
#> [1] "lfc"

if (interactive()) {
    iSEE(se, initial=list(MAPlot()))
}