--- a
+++ b/preprocessing/Preprocessing_scRNA_CLL_GSE111014.R
@@ -0,0 +1,22 @@
+library(Matrix)
+library(Seurat)
+library(dplyr)
+source("/research/users/ppolonen/git_home/common_scripts/scRNA/functions.scRNA.analysis.R")
+
+setwd("/research/groups/sysgen/PROJECTS/HEMAP_IMMUNOLOGY/petri_work/scRNA")
+
+name="CLL_D0"
+
+# DATA:
+m=data.matrix(Matrix::readMM("/research/groups/biowhat_share/public_data/scRNAseq/GSE111014_CLL/GSE111014_matrix.mtx"))
+colnames(m)=scan("/research/groups/biowhat_share/public_data/scRNAseq/GSE111014_CLL/GSE111014_barcodes.tsv", "a")
+genes=data.table::fread("/research/groups/biowhat_share/public_data/scRNAseq/GSE111014_CLL/GSE111014_genes.tsv", data.table = F, header = F)[,2]
+rownames(m)=make.unique(genes)
+
+# filter
+m=m[,grepl("d0", colnames(m))]
+
+# using the function:
+batch=gsub(".*.-seq_", "", colnames(m))
+
+test1=sc.data.analysis(scmat = m, regress.cell.label = batch, batch.correction.method = "MNNcorrect", name="CLL_D0", nr.pcs = 22, check.pcs=F, plot.umap = T, nFeature.min = 200, nFeature.max = 4000, percent.mitoDNA = 10)
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