scRNA-seq_analysis

pipelines/04_merge_seurat_objects/merge_seurat_objects.R

@@ -0,0 +1,90 @@
+args = commandArgs(trailingOnly=T)
+args = paste(args, collapse = "")
+args = unlist(strsplit(args, ";"))
+if(length(args) != 5){
+  stop('This pipeline requires 5 parameters: seurat.addrs (list of file names)\nappend_tag (boolean)\ntags_to_append (list of tags)\nappend_tags_at (list of meta.data columns where to append the tags)\nsave (file name to save the data at)')
+}
+
+arguments.list = "
+seurat.addrs.arg    = args[1]
+append_tag.arg      = args[2]
+tags_to_append.arg  = args[3]
+append_tags_at.arg  = args[4]
+save.at.arg         = args[5]
+"
+eval(parse(text = arguments.list))
+
+arguments.list = unlist(strsplit(arguments.list, "\n"))
+arguments.list = arguments.list[!(arguments.list == "")]
+
+for(n in 1:length(arguments.list)){
+  argument = arguments.list[n]
+  argument = gsub(pattern=" ", replacement="", x=argument)
+  argument.name = unlist(strsplit(argument, "="))[1]
+  variable.name = gsub(pattern=".arg", replacement="", argument.name)
+  argument.content = eval(parse(text = argument.name))
+  eval(parse(text = argument.content))
+  if (!exists(variable.name)){
+    stop(sprintf("Argument %s not passed. Stopping ... ", variable.name))
+  }
+}
+
+for(n in 1:length(seurat.addrs)){
+  seurat.addrs[n] = file.path("../../data", seurat.addrs[n])
+}
+save.at = file.path("../../data", save.at)
+
+if(append_tag){
+  if ( length(tags_to_append) != length(seurat.addrs)){
+    stop("Number of tags is different from number of data objects. Stopping ... ")
+  }
+}
+
+library(Seurat)
+
+#######################################################################################################
+
+# init empty list to store the seurat objects
+store = list()
+
+# for each .RDS filename read the data and append object to the store lirest
+print("loading the datasets")
+for (i in 1:length(seurat.addrs)){
+  sprintf("Loaded %d out of %d", i, length(seurat.addrs))
+  seurat.obj = readRDS(seurat.addrs[i])
+  if(append_tag){
+    own.tag = tags_to_append[i]
+    for(md.index in 1:length(append_tags_at)){
+      md.name = append_tags_at[md.index]
+      code.line = sprintf("seurat.obj@meta.data$%s = paste(seurat.obj@meta.data$%s, '%s', sep = '_')", md.name, md.name, own.tag)
+      eval(parse(text = code.line))
+    }
+  }
+  store[[i]] = seurat.obj
+  print(store[[i]])
+}
+
+# merge first 2 objects
+print("Merging the first 2 datasets")
+seurat.obj = MergeSeurat(object1=store[[1]], object2=store[[2]], project="None", min.cells=0, min.genes=0)
+# add the rest of the seurat objects
+if(length(store) > 2){
+  for (j in 3:length(store)){
+    sprintf("Adding dataset %d", j)
+    seurat.obj = MergeSeurat(object1=seurat.obj, object2=store[[j]], project="None", min.cells=0, min.genes=0)
+  }
+}
+rm(store)
+
+print("normalizing data ... ")
+seurat.obj = NormalizeData(object = seurat.obj, normalization.method = "LogNormalize", scale.factor = 10000)
+print("Computing variable genes ... ")
+seurat.obj = FindVariableGenes(object = seurat.obj, mean.function = ExpMean, 
+                                dispersion.function = LogVMR, x.low.cutoff = .0125, 
+                                x.high.cutoff = 3, y.cutoff = .625)
+print("Scaling data ...")
+seurat.obj = ScaleData(object=seurat.obj)
+print("Saving data ... ")
+saveRDS(seurat.obj, save.at)
+
+print("Ended beautifully ... ")

pipelines/04_merge_seurat_objects/merge_seurat_objects.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+#$ -cwd
+#$ -N merge_seurat_objects
+#$ -V
+#$ -l h_rt=23:59:59
+#$ -l h_vmem=200G
+
+if [ "$#" -ne 1 ]; then
+    echo "Illegal number of parameters"
+    exit 1
+fi
+
+Rscript merge_seurat_objects.R $1
+
+echo "End on `date`"