Global DE prefixes

Get or set patterns for acceptable names of rowData columns related to a differential expression analysis. These functions are deprecated; use their counterparts in ?"registerPValuePatterns" instead.

Usage

getPValuePattern()

getLogFCPattern()

getAveAbPattern()

setPValuePattern(value)

setLogFCPattern(value)

setAveAbPattern(value)

Arguments

value: A character vector containing the acceptable prefixes for each statistic.

Value

getPValuePattern returns the patterns for acceptable column names for p-values.

getLogFCPattern returns the patterns for acceptable column names for log-fold changes.

getAveAbPattern returns the patterns for acceptable column names for the average abundances.

The corresponding setters set the global parts for each statistic and return NULL invisibly.

Details

These utilities allow users to easily get and set the patterns of acceptable fields in all VolcanoPlots, MAPlots and LogFCLogFCPlots at once. Any global settings only take effect (i) during setup of the iSEE application and (ii) if the first panel of each class does not have existing values in the "PValueFields", "LogFCFields" or "AveAbFields" slots (which take precedence if present).

Each of these global settings are treated as patterns for partial matching. For the "PValue" pattern, columns with the names "PValue.X" and "X.PValue" will be considered acceptable matches. All partial matching must be exact - regular expressions are not supported.

Author

Aaron Lun

Examples

old <- getPValuePattern()

setPValuePattern(LETTERS)
#> Warning: 'setPValuePattern' is deprecated.
#> Use 'registerPValuePatterns' instead.
#> See help("Deprecated")
getPValuePattern()
#>  [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" "Q" "R" "S"
#> [20] "T" "U" "V" "W" "X" "Y" "Z"

setPValuePattern(old)
#> Warning: 'setPValuePattern' is deprecated.
#> Use 'registerPValuePatterns' instead.
#> See help("Deprecated")