preprocessNwaTS: A preprocessing method for a GSCABatch object of Time-series...

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

Description

This function will do basic preprocessing for each NWA object of 'nwaList'.

Usage

preprocessNwaTS(
  object,
  species = "Hs",
  initialIDs = "SYMBOL",
  keepMultipleMappings = TRUE,
  duplicateRemoverMethod = "max",
  verbose = TRUE
)

Arguments

object	An NWABatch object.
species	A single character value specifying the species for which the data should be read.
initialIDs	A single character value specifying the type of initial identifiers for input nwaList.
keepMultipleMappings	A single logical value. If TRUE, the function keeps the entries with multiple mappings (first mapping is kept). If FALSE, the entries with multiple mappings will be discarded.
duplicateRemoverMethod	A single character value specifying the method to remove the duplicates. See duplicateRemover for details.
verbose	A single logical value specifying whether to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE), default is TRUE.

Value

In the end, this function will return an updated list of NWA object.

See Also

preprocess

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})

## create an object of class 'NWABatch' with phenotypes
nwaTS <- NWABatch(expInfor = expInfor, pvalueTS = pvalueTS, phenotypeTS = phenotypeTS)

## preprocess nwaTS
nwaTS1 <- preprocessNwaTS(nwaTS, species="Hs", initialIDs="SYMBOL",
                         keepMultipleMappings=TRUE, duplicateRemoverMethod="max")

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