#make individual Seurat objects library(Seurat) ###1mFB_406RR2_0202 SampleName <- rep ("1mFB_406RR2_0202", ncol(data.1mFB_406RR2_0202)) SampleName2 <- rep ("1mFB_406RR2_02", ncol(data.1mFB_406RR2_0202)) Genotype <- rep ("wildtype", ncol(data.1mFB_406RR2_0202)) Genotype2 <- rep ("406RR", ncol(data.1mFB_406RR2_0202)) Age <- rep ("1m", ncol(data.1mFB_406RR2_0202)) BrainRegion <- rep ("FB", ncol(data.1mFB_406RR2_0202)) BatchReceived <- rep ("2", ncol(data.1mFB_406RR2_0202)) SequencingRun <- rep ("2", ncol(data.1mFB_406RR2_0202)) sampleinfo1mFB_406RR2_0202 <- data.frame(row.names = colnames(data.1mFB_406RR2_0202), SampleName, SampleName2, Genotype, Genotype2, Age, BatchReceived, SequencingRun) seurat.1mFB_406RR2_0202 <- CreateSeuratObject (counts = data.1mFB_406RR2_0202, meta.data = sampleinfo1mFB_406RR2_0202) ###1mFB_406RW2_0202 SampleName <- rep ("1mFB_406RW2_0202", ncol(data.1mFB_406RW2_0202)) SampleName2 <- rep ("1mFB_406RW2_02", ncol(data.1mFB_406RW2_0202)) Genotype <- rep ("406RW", ncol(data.1mFB_406RW2_0202)) Genotype <- rep ("406RW", ncol(data.1mFB_406RW2_0202)) ####this is a mistake - should be "Genotype2" Age <- rep ("1m", ncol(data.1mFB_406RW2_0202)) BrainRegion <- rep ("FB", ncol(data.1mFB_406RW2_0202)) BatchReceived <- rep ("2", ncol(data.1mFB_406RW2_0202)) SequencingRun <- rep ("2", ncol(data.1mFB_406RW2_0202)) sampleinfo1mFB_406RW2_0202 <- data.frame(row.names = colnames(data.1mFB_406RW2_0202), SampleName, SampleName2, Genotype, Genotype2, Age, BatchReceived, SequencingRun) seurat.1mFB_406RW2_0202 <- CreateSeuratObject (counts = data.1mFB_406RW2_0202, meta.data = sampleinfo1mFB_406RW2_0202) ###2mFB_406RR2_0303 SampleName <- rep ("2mFB_406RR2_0303", ncol(data.2mFB_406RR2_0303)) SampleName2 <- rep ("2mFB_406RR2_03", ncol(data.2mFB_406RR2_0303)) Genotype <- rep ("wildtype", ncol(data.2mFB_406RR2_0303)) Genotype2 <- rep ("406RR", ncol(data.2mFB_406RR2_0303)) Age <- rep ("2m", ncol(data.2mFB_406RR2_0303)) BrainRegion <- rep ("FB", ncol(data.2mFB_406RR2_0303)) BatchReceived <- rep ("3", ncol(data.2mFB_406RR2_0303)) SequencingRun <- rep ("3", ncol(data.2mFB_406RR2_0303)) sampleinfo2mFB_406RR2_0303 <- data.frame(row.names = colnames(data.2mFB_406RR2_0303), SampleName, SampleName2, Genotype, Genotype2, Age, BatchReceived, SequencingRun) seurat.2mFB_406RR2_0303 <- CreateSeuratObject (counts = data.2mFB_406RR2_0303, meta.data = sampleinfo2mFB_406RR2_0303) ###2mFB_406RW2_0303 SampleName <- rep ("2mFB_406RW2_0303", ncol(data.2mFB_406RW2_0303)) SampleName2 <- rep ("2mFB_406RW2_03", ncol(data.2mFB_406RW2_0303)) Genotype <- rep ("406RW", ncol(data.2mFB_406RW2_0303)) Genotype2 <- rep ("406RW", ncol(data.2mFB_406RW2_0303)) Age <- rep ("2m", ncol(data.2mFB_406RW2_0303)) BrainRegion <- rep ("FB", ncol(data.2mFB_406RW2_0303)) BatchReceived <- rep ("3", ncol(data.2mFB_406RW2_0303)) SequencingRun<- rep ("3", ncol(data.2mFB_406RW2_0303)) sampleinfo2mFB_406RW2_0303 <- data.frame(row.names = colnames(data.2mFB_406RW2_0303), SampleName, SampleName2, Genotype, Genotype2, Age, BatchReceived, SequencingRun) seurat.2mFB_406RW2_0303 <- CreateSeuratObject (counts = data.2mFB_406RW2_0303, meta.data = sampleinfo2mFB_406RW2_0303) ###2mFB_406WW1_0303 SampleName <- rep ("2mFB_406WW1_0303", ncol(data.2mFB_406WW1_0303)) SampleName2 <- rep ("2mFB_406WW1_03", ncol(data.2mFB_406WW1_0303)) Genotype <- rep ("406WW", ncol(data.2mFB_406WW1_0303)) Genotype2 <- rep ("406WW", ncol(data.2mFB_406WW1_0303)) Age <- rep ("2m", ncol(data.2mFB_406WW1_0303)) BrainRegion <- rep ("FB", ncol(data.2mFB_406WW1_0303)) BatchReceived <- rep ("3", ncol(data.2mFB_406WW1_0303)) SequencingRun <- rep ("3", ncol(data.2mFB_406WW1_0303)) sampleinfo2mFB_406WW1_0303 <- data.frame(row.names = colnames(data.2mFB_406WW1_0303), SampleName, SampleName2, Genotype, Genotype2, Age, BatchReceived, SequencingRun) seurat.2mFB_406WW1_0303 <- CreateSeuratObject (counts = data.2mFB_406WW1_0303, meta.data = sampleinfo2mFB_406WW1_0303) ###3mFB_406RR2_0404 SampleName <- rep ("3mFB_406RR2_0404", ncol(data.3mFB_406RR2_0404)) SampleName2 <- rep ("3mFB_406RR2_04", ncol(data.3mFB_406RR2_0404)) Genotype <- rep ("wildtype", ncol(data.3mFB_406RR2_0404)) Genotype2 <- rep ("406RR", ncol(data.3mFB_406RR2_0404)) Age <- rep ("3m", ncol(data.3mFB_406RR2_0404)) BrainRegion <- rep ("FB", ncol(data.3mFB_406RR2_0404)) BatchReceived <- rep ("4", ncol(data.3mFB_406RR2_0404)) SequencingRun <- rep ("4", ncol(data.3mFB_406RR2_0404)) sampleinfo3mFB_406RR2_0404 <- data.frame(row.names = colnames(data.3mFB_406RR2_0404), SampleName, SampleName2, Genotype, Genotype2, Age, BatchReceived, SequencingRun) seurat.3mFB_406RR2_0404 <- CreateSeuratObject (counts = data.3mFB_406RR2_0404, meta.data = sampleinfo3mFB_406RR2_0404) ###3mFB_406RW2_0404 SampleName <- rep ("3mFB_406RW2_0404", ncol(data.3mFB_406RW2_0404)) SampleName2 <- rep ("3mFB_406RW2_04", ncol(data.3mFB_406RW2_0404)) Genotype <- rep ("406RW", ncol(data.3mFB_406RW2_0404)) Genotype2 <- rep ("406RW", ncol(data.3mFB_406RW2_0404)) Age <- rep ("3m", ncol(data.3mFB_406RW2_0404)) BrainRegion <- rep ("FB", ncol(data.3mFB_406RW2_0404)) BatchReceived <- rep ("4", ncol(data.3mFB_406RW2_0404)) SequencingRun <- rep ("4", ncol(data.3mFB_406RW2_0404)) sampleinfo3mFB_406RW2_0404 <- data.frame(row.names = colnames(data.3mFB_406RW2_0404), SampleName, SampleName2, Genotype, Genotype2, Age, BatchReceived, SequencingRun) seurat.3mFB_406RW2_0404 <- CreateSeuratObject (counts = data.3mFB_406RW2_0404, meta.data = sampleinfo3mFB_406RW2_0404) ###3mFB_406WW1_0404 SampleName <- rep ("3mFB_406WW1_0404", ncol(data.3mFB_406WW1_0404)) SampleName2 <- rep ("3mFB_406WW1_04", ncol(data.3mFB_406WW1_0404)) Genotype <- rep ("406WW", ncol(data.3mFB_406WW1_0404)) Genotype2 <- rep ("406WW", ncol(data.3mFB_406WW1_0404)) Age <- rep ("3m", ncol(data.3mFB_406WW1_0404)) BrainRegion <- rep ("FB", ncol(data.3mFB_406WW1_0404)) BatchReceived <- rep ("4", ncol(data.3mFB_406WW1_0404)) SequencingRun <- rep ("4", ncol(data.3mFB_406WW1_0404)) sampleinfo3mFB_406WW1_0404 <- data.frame(row.names = colnames(data.3mFB_406WW1_0404), SampleName, SampleName2, Genotype, Genotype2, Age, BatchReceived, SequencingRun) seurat.3mFB_406WW1_0404 <- CreateSeuratObject (counts = data.3mFB_406WW1_0404, meta.data = sampleinfo3mFB_406WW1_0404)