method-mr: robust Mahalanobis distance

In ococrook/bandle: An R package for the Bayesian analysis of differential subcellular localisation experiments

robust Mahalanobis distance

Description

These function implement the MR method of Itzhak et al

Usage

robustMahalanobis(delta)

reprodScore(x, y, method = c("pearson"))

mrMethod(objectCond1, objectCond2, method = "2017")

Arguments

delta	The difference profile to compute the squared mahalanobis distance
x	Numeric vector to compute reproducibility score
y	Numeric vector to compute reproducibility score
method	Correlation method. Default is Pearson
objectCond1	A list of MSnbase::MSnSets where each is an experimental replicate for the first condition, usually a control
objectCond2	A list of MSnbase::MSnSets where each is an experimental replicate for the second condition, usually a treatment

Value

The squared Mahalanobis distance

The R score

The MR score of the Ithzak et al. 2016/2017

Examples

## Generate some example data
library("pRolocdata")
data("tan2009r1")
set.seed(1)
tansim <- sim_dynamic(object = tan2009r1, 
                      numRep = 4L,
                      numDyn = 100L)
data <- tansim$lopitrep
control <- data[1:2]
treatment <- data[3:4]

## compute delta matrix
deltaMatrix <- exprs(control[[1]]) - exprs(treatment[[1]])
res <- bandle:::robustMahalanobis(deltaMatrix)
##' @examples 
## Generate some example data
library("pRolocdata")
data("tan2009r1")
set.seed(1)
tansim <- sim_dynamic(object = tan2009r1, 
                      numRep = 4L,
                      numDyn = 100L)
data <- tansim$lopitrep
control <- data[1:2]
treatment <- data[3:4]

## compute delta matrix
deltaMatrix1 <- exprs(control[[1]]) - exprs(treatment[[1]])
deltaMatrix2 <- exprs(control[[2]]) - exprs(treatment[[2]])
mr_score <- bandle:::reprodScore(deltaMatrix1, deltaMatrix2)
library(pRolocdata)
data("tan2009r1")
set.seed(1)
tansim <- sim_dynamic(object = tan2009r1, 
                    numRep = 6L,
                   numDyn = 100L)
d1 <- tansim$lopitrep
control1 <- d1[1:3]
treatment1 <- d1[4:6]
mr1 <- mrMethod(objectCond1 = control1, objectCond2 = treatment1)
plot(mr1$Mscore, mr1$Rscore, pch = 21, 
     xlab = "MScore", ylab = "RScore")

ococrook/bandle documentation built on Nov. 4, 2024, 12:27 a.m.