registerDEFields {iSEEu} | R Documentation

## Register DE-related fields

### Description

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`.

### 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 usual 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 `defaults`.

### 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.

### Author(s)

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)
    se <- registerAveAbFields(se, "average")
    getAveAbFields(se)
    se <- registerLogFCFields(se, "lfc")
    getLogFCFields(se)

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

[Package iSEEu version 1.4.0 Index]