buildSignatureMatrixMAST: Signature Matrix Using MAST

In DWLS: Gene Expression Deconvolution Using Dampened Weighted Least Squares

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)

DWLS documentation built on May 24, 2022, 5:07 p.m.