DEAnalysisSeuratIdents: Differential Expression with Idents (Seurat)

In DWLS: Gene Expression Deconvolution Using Dampened Weighted Least Squares

Differential Expression with Idents (Seurat)

Description

This function calculates the differential expression values along with identifying the Idents (through Seurat). The output is saved in an RData file for each unique identity (id).

Usage

DEAnalysisSeuratIdents(scdata, id, path)

Arguments

scdata	The gene expression datafarme
id	The unique identities within the data
path	The path for the RData results

Value

An RData file with the differential expression analysis results for each unique id.

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"))

#Old Method
#load("data/dataSC_3.RData")
#load("data/trueLabels.RData")
#load("data/dataBulk.RData") #read in bulk data for WT1 (control condition #1)
#load("data/labels.RData") #read in single-cell labels from clustering

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 deconvolution
#Seurat_test2 <- DEAnalysisSeuratIdents(dataSC, labels, "results")

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