NWABatch: An S4 class for Time series data package in NetWork Analysis...

In CityUHK-CompBio/HTSanalyzeR2: HTSanalyzeR2: An R package for functional annotation, network analysis and time series analysis of high-throughput data

Description

This S4 class packages time-series data for further time series analysis. To put it more clearly, it'll finally initialize a list of NWA objects for further analyses.

Usage

NWABatch(expInfor, pvalueTS, phenotypeTS = list(), interactome = NA)

Arguments

expInfor	A character matrix contains experiment information with each experiment in row and information in column. Should at least contain two columns named as 'ID' and 'Desription'.
pvalueTS	A list of pvalues, each element of this list is a numeric vector pvalues named by gene identifiers for each time point. Note: the order of each element of this list must match the order of 'expInfor' ID.
phenotypeTS	A list of phenotypes, each element of this list is a numeric vector phenotypes named by gene identifiers for each time point. Note: the order of each element of this list must match the order of 'expInfor' ID. When it is available, nodes in identified subnetworks would be coloured by it (red:+, blue:- as default). Otherwise, all nodes in the subnetworks would have no difference.
interactome	An object of class igraph.

Value

This function will create a new object class 'NWABatch'.

Slots

listOfNWA

A list of 'NWA' object.

See Also

NWA-class, preprocessNwaTS, interactomeNwaTS, analyzeNwaTS

Examples

data(d7, d13, d25)

## generate expInfor to describe the information of time series data
expInfor <- matrix(c("d7", "d13", "d25"), nrow = 3, ncol = 2,
                   byrow = FALSE, dimnames = list(NULL, c("ID", "Description")))

## package pvalueTS into a list of pvalues
datalist <- list(d7, d13, d25)
pvalueTS <- lapply(datalist, function(x){
                   tmp <- as.vector(x$neg.p.value)
                   names(tmp) <- x$id
                   tmp})

## package phenotypeTS into a list of phenotypes if you want to color nodes by it,
## otherwise ignore it!
phenotypeTS <- lapply(datalist, function(x) {
                      tmp <- as.vector(x$neg.lfc)
                      names(tmp) <- x$id
                      tmp})
## Example1: create an object of class 'NWABatch' with phenotypes
nwaTS <- NWABatch(expInfor = expInfor, pvalueTS = pvalueTS, phenotypeTS = phenotypeTS)

## Example2: create an object of class 'NWABatch' without phenotypes
nwaTS <- NWABatch(expInfor = expInfor, pvalueTS = pvalueTS)

CityUHK-CompBio/HTSanalyzeR2 documentation built on Dec. 3, 2020, 2:35 a.m.