sort_uwmwRes: Sort and order method for uWMWRes objects

In unifiedWMWqPCR: Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data

Description

This functions provide sorting functionality for uwmwRes objects. It allows to sort the values in the object in order to get the genes with the highest OR, lowest p value, ... The function uses order underneath

Usage

unorder(x, ...)

## S4 method for signature 'uwmwRes'
sort(x, decreasing = FALSE, which = c("or", "p", "se",
  "name", "z"), na.last = TRUE, ...)

## S4 method for signature 'ANY'
unorder(x, ...)

## S4 method for signature 'uwmwRes'
unorder(x, ...)

## S4 method for signature 'uwmwRes'
order(..., na.last = TRUE, decreasing = FALSE,
  method = c("auto", "shell", "radix"))

Arguments

x	a uwmwRes object
...	currently ignored
decreasing	a logical value indicating whether values should be sorted in increasing or decreasing order.
which	a character value indicating on which values should be used to sort on. The possible values are: "or" for sorting on the odds ratio, "p" for sorting on the p value, "se" for sorting on the standard error or "name" for sorting on the gene names.
na.last	a logical value indicating whether NA results should be sorted at the end. See order for more information.
method	Argument of the generic, ignored here. See also order

Details

The function does not change the internal order, but changes the slot id in the object. This slot is used by other functions to give the requested values

Value

sort returns a sorted uwmwRes object.

See Also

The functions is.unsorted, orderedBy and getOrder to check on the ordered state of a uwmwRes object.

order returns the order of the uwmwRes object.

unorder returns a uwmwRes object with the order removed.

Examples

data(NBmat)
NBtest <- uWMW(NBmat, groups=NBgroups)
NBsort <- sort(NBtest,which="name")
NBsort[1:10]

unifiedWMWqPCR documentation built on Nov. 8, 2020, 6:05 p.m.