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constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
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For loops don't seem to work with soupX #145

Open Kenneth-new-user opened 7 months ago

Kenneth-new-user commented 7 months ago

I have multiple matrix files that I would like to run through with SoupX but the following code stops after the first iteration. Ideally I would want to read through the files in data/Matrices and then save the outputs in data/Matrices/soupX.

library(Seurat)
library(SoupX)

Files = c("file1", "file2", "file3", "file4")

for(f in Files) {
  data.dir  = paste("~/data/Matrices//", f, "/filtered_feature_bc_matrix",sep="")
  InPath  = paste("~/data/Matrices/", f, sep="")
  OutFile = paste("~/data/Matrices/soupx/", f, sep="")
  data <- Read10X(data.dir = data.dir)
  data = CreateSeuratObject(counts = data)
  data <- NormalizeData(data)
  data <- FindVariableFeatures(data, selection.method = "vst", nfeatures = 2000)
  all.genes <- rownames(data)
  data <- ScaleData(data, features = all.genes)
  data <- RunPCA(data, features = VariableFeatures(object = data))
  data <- FindNeighbors(data, dims = 1:10)
  data <- FindClusters(data, resolution = 0.5)
  sc = load10X(InPath)
  sc = setClusters(sc, setNames(data$seurat_clusters, colnames(data)))
  sc = autoEstCont(sc)
  out = adjustCounts(sc, roundToInt=TRUE)
  DropletUtils:::write10xCounts(OutFile, out)
}