buildSignatureMatrixMAST {DWLS}

Signature Matrix Using MAST

Description

This function builds a signature matrix using genes identified by the DEAnalysisMAST() function.

Usage

buildSignatureMatrixMAST(
  scdata,
  id,
  path,
  diff.cutoff = 0.5,
  pval.cutoff = 0.01,
  f = 200
)

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

f

The maximum number of genes (when creating the signature matrix, need to reduce number of genes, between 50:f number of significant genes are chosen). If not set, this number is automatically set to 200.

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]
  }

#Run on local w/ inst/extdata/results folder
#Signature <-
#buildSignatureMatrixMAST(
#dataSC,labels,"inst/extdata/results",diff.cutoff = 0.5,pval.cutoff = 0.01)