DEAnalysisSeurat {DWLS} | R Documentation |
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")
[Package DWLS version 0.1.0 Index]