--- a
+++ b/Cydar/01_fastMNN_ADT.R
@@ -0,0 +1,49 @@
+library(batchelor)
+library(scater)
+library(BiocParallel)
+library(BiocSingular)
+
+adtf <- "../../Newcastle/combined_dec_ADT_SCE.RDS"
+
+adt <- readRDS(adtf)
+
+# There are some samples with no antibody signal, cool
+rmSamples <- c("MH8919226","MH8919227","MH8919228","MH8919229","MH8919230","MH8919231","MH8919232","MH8919233")
+
+# removing doublets identified by Mike and Kelvin
+mk <- read.table("../data/doublets/Tcell_doublets.tsv",header=FALSE,sep="\t",stringsAsFactors=FALSE)
+kl <- read.csv("../data/doublets/Karsten_doublets.csv",stringsAsFactors=FALSE)
+dbls <- c(kl$doublets[kl$doublets!=""], mk$V1)
+
+rmBcs <- colnames(adt)[adt$initial_clustering=="Doublet" | adt$sample_id %in% rmSamples]
+rmBcs <- c(rmBcs,dbls)
+
+
+
+adt <- adt[,!colnames(adt) %in% rmBcs]
+
+set.seed(42)
+adt1 <- adt[,adt$Site=="Cambridge"]
+adt2 <- adt[,adt$Site=="Ncl"]
+adt3 <- adt[,adt$Site=="Sanger"]
+
+
+param <- MulticoreParam(workers=4)
+print("Starting MNN")
+set.seed(300)
+mnncor <- batchelor::fastMNN(adt2,adt1,adt3,
+		     BPPARAM=param, # commented this out for singularity
+		     k=20,
+		     d=50,
+		     merge.order=c(1,2,3),
+		     BSPARAM=IrlbaParam(deferred=TRUE),
+		     assay.type="counts",
+		     #                      BNPARAM=AnnoyParam(),
+		     cos.norm=TRUE, # prob necesarry
+		     correct.all=TRUE)
+print("Done MNN")
+
+m.cor <- assay(mnncor,"reconstructed")
+m.cor <- m.cor[,colnames(adt)]
+assay(adt,"reconstructed") <- m.cor
+saveRDS(adt,"../data/combined_dec_ADT_MNNcorrected.RDS")