MASTSignatureMatrixGivenDE {DWLS}

Build Signature matrix using MAST given a differential expression matrix

Description

This function builds a signature matrix using a pre-created differential expression matrix. The input matrix must have the same format as the DEAnalysisMAST() function and must be saved as an RData file ending with _MIST. The file must be named identity_MIST.RData. See exampledata_MIST.RData for more information (inst/man).

Usage

MASTSignatureMatrixGivenDE(
  scdata,
  id,
  path,
  diff.cutoff = 0.5,
  pval.cutoff = 0.01
)

Arguments

scdata

The data

id

The identities of the genes

path

The path to the file results

diff.cutoff

This is automatically set to 0.5

pval.cutoff

This is automatically set to 0.01

Value

Signature Matrix built using the MAST algorithm

Examples

#dataSC
#url <- "https://github.com/sistia01/DWLS/raw/main/inst/extdata/dataSC.RData"
#dest <- "data/dataSC.RData"
#load(download.file(url, tempfile(data/dataSC.RData))
#load("dataSC.RData")
#SOLUTION
load(system.file("extdata", "dataSC.RData", package = "DWLS"))

#dataBulk
#url <- "https://github.com/sistia01/DWLS/raw/main/inst/extdata/dataBulk.RData"
#dest <- "data/dataBulk.RData"
#load(download.file(url, tempfile(dest)))
#load("data/dataBulk.RData")
load(system.file("extdata", "dataBulk.RData", package = "DWLS"))

#labels
#url <- "https://github.com/sistia01/DWLS/raw/main/inst/extdata/labels.RData"
#dest <- "data/labels.RData"
#download.file(url, dest)
#load("data/labels.RData")
load(system.file("extdata", "labels.RData", package = "DWLS"))

#data('trueLabels', package = "DWLS")
#url <- "https://github.com/sistia01/DWLS/raw/main/inst/extdata/trueLabels.RData"
#dest <- "data/trueLabels.RData"
#download.file(url, dest)
#load("data/trueLabels.RData")
load(system.file("extdata", "trueLabels.RData", package = "DWLS"))

labels<-trueLabels

#Change to real labels
newcat<-c("NonCycISC","CycISC","TA","Ent","PreEnt","Goblet",
"Paneth","Tuft","EE")
for (i in 1:length(newcat)){
  labels[which(labels==(i-1))]<-newcat[i]
  }
#Results in inst/extdata/results -- run on local
#Signature<-buildSignatureMatrixMAST(dataSC,labels,"results",
# diff.cutoff=0.5,pval.cutoff=0.01)