library(Seurat)We have separately analyzed the five major subsets of cells and annotated the cell clusters in them. Now we want them together to explore all the data globally.
tcells <- readRDS(file = '~/000_GitHub/ibd-bcn_single_cell/Analysis of our data/02_Samples_Together/SUBSETS/ON_THEIR_OWN/tcells_annotated.RDS')
epi <- readRDS(file = '~/000_GitHub/ibd-bcn_single_cell/Analysis of our data/02_Samples_Together/SUBSETS/ON_THEIR_OWN/epi_annotated.RDS')
stroma <- readRDS(file = '~/000_GitHub/ibd-bcn_single_cell/Analysis of our data/02_Samples_Together/SUBSETS/ON_THEIR_OWN/stroma_annotated.RDS')
plasmas <- readRDS(file = '~/000_GitHub/ibd-bcn_single_cell/Analysis of our data/02_Samples_Together/SUBSETS/ON_THEIR_OWN/plasmas_annotated.RDS')
myeloids <- readRDS(file = '~/000_GitHub/ibd-bcn_single_cell/Analysis of our data/02_Samples_Together/SUBSETS/ON_THEIR_OWN/myeloids_annotated.RDS')
together <- merge(epi, myeloids)
together <- merge(together, tcells)
together <- merge(together, stroma)
together <- merge(together, plasmas)Now we have an object with 46700 cells and 33382 features. We save the object for futures analysis:
saveRDS(together, file = 'SUBSETS/ON_THEIR_OWN/together_annotated.RDS')