bandle-plots-translocations-table: Generate a table of differential localisations

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

Generate a table of differential localisations

Description

This function produces a table summarising differential localisation results between two experiments

Usage

plotTable(params, all = FALSE, fcol)

Arguments

params	An instance of class bandleParams or an instance of class MSnSetList of length 2.
all	A logical specifying whether to count all proteins or only show those that have changed in location between conditions. Default is FALSE.
fcol	If params is a list of MSnSets. Then fcol must be defined. This is a character vector of length 2 to set different labels for each dataset. If only one label is specified, and the character is of length 1 then this single label will be used to identify the annotation column in both datasets.

Value

Returns a summary table of translocations of proteins between conditions.

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]

## fit GP params
gpParams <- lapply(tansim$lopitrep, function(x) 
fitGPmaternPC(x, hyppar = matrix(c(0.5, 1, 100), nrow = 1)))

## run bandle
res <- bandle(objectCond1 = control,
              objectCond2 = treatment, 
              gpParams = gpParams,
              fcol = "markers",  
              numIter = 5L, 
              burnin = 1L, 
              thin = 2L,
              numChains = 2, 
              BPPARAM = SerialParam(RNGseed = 1),
              seed = 1)
               
## Process bandle results
bandleres <- bandleProcess(res)

## Tabulate results
plotTable(bandleres)  

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