add project metadata

DESCRIPTION

@@ -1,12 +1,14 @@
 Package: FastIntegration
 Type: Package
-Title: What the Package Does (Title Case)
+Title: Fast Integration of Single-cell Data
 Version: 0.1.0
-Author: Who wrote it
-Maintainer: The package maintainer <[email protected]>
-Description: More about what it does (maybe more than one line)
-    Use four spaces when indenting paragraphs within the Description.
-License: What license is it under?
+Author: c(
+  person(given = "Mengwei", family = "Li", email = "[email protected]", role = "aut"),
+  person(given = "Xiaomeng", family = "Zhang", email = "[email protected]", role = "aut"),
+  person(given = "Jinmiao", family = "Chen", email = "[email protected]", role = "aut")
+  )
+Description: FastIntegrate integrates thousands of scRNA-seq datasets and outputs batch-corrected values for downstream analysis
+License: GPL-3
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.1.1

NAMESPACE

@@ -1,5 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+export(BuildIntegrationFile)
+export(FastFindAnchors)
+export(FastIntegration)
 import(Matrix)
 import(Seurat)
 import(SeuratObject)

R/FastFindAnchors.R

@@ -4,6 +4,7 @@
 #' @import dplyr
 #' @import Matrix
 #' @importFrom utils getFromNamespace
+#' @export
 FastFindAnchors = function(
   tmp.dir = NULL,
   nCores = NULL,
@@ -62,8 +63,10 @@ FastFindAnchors = function(
   ncel.min = pmin(ncell.a, ncell.b)
   similarity.matrix = similarity.matrix/ncel.min
   similarity.matrix[upper.tri(x = similarity.matrix, diag = TRUE)] = NA
+  BuildSampleTree = getFromNamespace("BuildSampleTree", "Seurat")
+  sample.tree = BuildSampleTree(similarity.matrix)
 
-  saveRDS(similarity.matrix, paste0(tmp.dir, "/FastIntegrationTmp/others/similarity_matrix.rds"), compress = F)
+  saveRDS(sample.tree, paste0(tmp.dir, "/FastIntegrationTmp/others/sample_tree.rds"), compress = F)
   saveRDS(all.anchors, paste0(tmp.dir, "/FastIntegrationTmp/anchors/anchors.rds"), compress = F)
   return(NULL)
 }
@@ -133,7 +136,7 @@ FindAnchorsPair = function(
   return(anchors)
 }
 
-
+#' @export
 BuildIntegrationFile = function(
   rna.list,
   tmp.dir = NULL,

R/FastIntegration.R

@@ -1,16 +1,20 @@
 #' @import tictoc
+#' @export
 FastIntegration = function(
   tmp.dir = NULL,
   features.to.integrate = NULL,
   input.pca,
   nn.k = 100,
   slot = c("data", "counts")
 ) {
+  setDTthreads(threads = 1L)
+  message("Reading anchor file")
   anchors = readRDS(paste0(tmp.dir, "/FastIntegrationTmp/anchors/anchors.rds"))
   offsets = readRDS(paste0(tmp.dir, "/FastIntegrationTmp/others/offsets.rds"))
   obj.lengths = readRDS(paste0(tmp.dir, "/FastIntegrationTmp/others/object_ncells.rds"))
-  similarity.matrix = readRDS(paste0(tmp.dir, "/FastIntegrationTmp/others/similarity_matrix.rds"))
-  sample.tree = Seurat:::BuildSampleTree(similarity.matrix = similarity.matrix)
+  sample.tree = readRDS(paste0(tmp.dir, "/FastIntegrationTmp/others/sample_tree.rds"))
+
+  message("Reading rna list file")
   object.list = list()
   for (i in 1:length(obj.lengths)) {
     a = readRDS(paste0(tmp.dir, "/FastIntegrationTmp/raw/", i, ".rds"))