uwmw_Accessors: Extract info from uwmwRes and uwmwEstimate objects

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

Extract info from uwmwRes and uwmwEstimate objects

Description

This help file describes different ways to access the slots and values contained in uwmwRes objects resulting from calls to uWMW, and in uwmwEstimate objects resulting from calls to getEstimate.

Usage

type(x)

## S4 method for signature 'uwmwRes'
type(x)

## S4 method for signature 'uwmwEstimate'
type(x)

## S4 method for signature 'uwmwRes'
housekeeping(x)

## S4 method for signature 'uwmwEstimate'
housekeeping(x)

## S4 method for signature 'uwmwRes'
names(x)

## S4 method for signature 'uwmwEstimate'
names(x)

## S4 method for signature 'uwmwRes'
logor(x, ordered = TRUE)

## S4 method for signature 'uwmwRes'
se(x, ordered = TRUE)

## S4 method for signature 'uwmwEstimate'
se(x)

## S4 method for signature 'uwmwRes'
oddsRatio(x, ordered = TRUE)

## S4 method for signature 'uwmwRes'
zval(x, ordered = TRUE)

## S4 method for signature 'uwmwRes'
pval(x, ordered = TRUE)

## S4 method for signature 'uwmwRes'
coef(object)

## S4 method for signature 'uwmwRes'
vcov(object)

## S4 method for signature 'uwmwEstimate'
ref(x)

## S4 method for signature 'uwmwEstimate'
esttype(x)

## S4 method for signature 'uwmwRes'
getOrder(x)

is.unsorted(x, na.rm = FALSE, strictly = FALSE)

## S4 method for signature 'uwmwRes'
orderedBy(x)

## S4 method for signature 'uwmwEstimate'
orderedBy(x)

## S4 method for signature 'uwmwRes'
groupinfo(x)

## S4 method for signature 'uwmwEstimate'
groupinfo(x)

## S4 method for signature 'uwmwEstimate'
length(x)

## S4 method for signature 'uwmwRes'
length(x)

Arguments

x	a uwmwRes object or a uwmwEstimate object.
ordered	logical value. If set to FALSE, the extracted values are given in the original order, also after a uwmwRes object has been ordered using sort. Defaults to TRUE
object	see x
na.rm	for compatibility with the base function is.unsorted. Ignored for uwmwRes objects.
strictly	for compatibility with the base function is.unsorted. Ignored for uwmwRes objects.

Value

type(x) returns the type of uWMW carried out (i.e. O or H for using overall respectively housekeeping expression as a reference.)

housekeeping(x) returns the content of the housekeeping slot from the object. Or, in case of overall normalization, it returns NULL.

names(x) returns the names of the genes in the object, and in the order defined in the object.

logor(x) returns a numeric vector with the log OR values.

se(x) returns a numeric vector with the standard errors on the logor.

oddsRatio(x) returns a numeric vector with the odds ratios.

zval(x) returns a numerical vector with the Z values contained in the object.

pval(x) returns a numerical vector containing the p values in the object.

orderedBy(x) returns the slot by which the object is ordered (i.e. the value of the slot orderedBy)

groupinfo(x) returns the groupinfo slot, i.e. a character vector of length 2 that indicates in which order the groups are compared by uWMW.

See Also

uwmw_Extract for matrix like extraction of data.

Examples

data(NBmat)
NBtest <- uWMW(NBmat,NBgroups)
coef(NBtest)[1:10]
type(NBtest)

# With a sorted object
NBsort <- sort(NBtest, which="p")
is.unsorted(NBtest)
is.unsorted(NBsort)
orderedBy(NBsort)

# On an Estimate object
NBlogodds <- getEstimate(NBsort,"logodds")
se(NBlogodds)
# and so on...

CenterForStatistics-UGent/unifiedWMWqPCR documentation built on Oct. 28, 2024, 2:34 p.m.