DEAnalysisSeurat: Differential Expression without Idents (Seurat)

In DWLS: Gene Expression Deconvolution Using Dampened Weighted Least Squares

Differential Expression without 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

DEAnalysisSeurat(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 and rds 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"
#download.file(url, dest)
#load("data/dataSC.RData")
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"
#download.file(url, 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

#Old Method
#load("data/dataBulk.RData") #read in bulk data for WT1 (control condition #1)
#load("data/labels.RData") #read in single-cell labels from clustering
#data('dataSC_3', package = "DWLS")
#dataSC <- dataSC_3

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 -- run on local
#Results in inst/extdata/results
Seurat_DE <- DEAnalysisSeurat(dataSC, labels, "inst/extdata/results")

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