add CELLiD

DESCRIPTION

@@ -1,26 +1,31 @@
-Package: FastIntegration
 Type: Package
+Package: FastIntegration
 Title: Fast Integration of Single-cell Data
 Version: 1.1.0
-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
+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
 Depends:
+    data.table,
     R (>= 4.0.0),
     Seurat (>= 4.0.0),
-    SeuratObject (>= 4.0.0),
-    data.table
+    SeuratObject (>= 4.0.0)
 Imports:
-    Matrix,
-    tictoc,
     dplyr,
+    Matrix,
     parallel,
-    pbmcapply
-LinkingTo: Rcpp (>= 0.11.0), RcppEigen
+    pbmcapply,
+    Rfast,
+    tictoc
+LinkingTo: 
+    Rcpp (>= 0.11.0),
+    RcppEigen
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.2.0

NAMESPACE

@@ -1,14 +1,18 @@
 # Generated by roxygen2: do not edit by hand
-export(FindSampleByMetadata)
-export(DownloadDiscoData)
+
 export(BuildIntegrationFile)
+export(CELLiD)
+export(DownloadDiscoData)
 export(FastFindAnchors)
 export(FastIntegration)
+export(FindSampleByMetadata)
 export(OneStopIntegration)
 import(Matrix)
 import(Rcpp)
 import(RcppEigen)
+import(jsonlite)
 import(tictoc)
+importFrom(Rfast,rowVars)
 importFrom(dplyr,`%>%`)
 importFrom(dplyr,arrange)
 importFrom(dplyr,desc)

R/CELLiD.R

@@ -0,0 +1,50 @@
+#' @importFrom Rfast rowVars
+#' @export
+CELLiD = function(input.data, ref.data) {
+
+  genes = intersect(rownames(input.data), rownames(ref.data))
+  if (length(genes) <= 2000) {
+    stop("Too few overlapped gene between input data and reference!")
+  } else {
+
+    input.data = input.data[genes,,drop = F]
+    ref.data = ref.data[genes,,drop = F]
+    predicted.cell = pbmclapply(
+      1:ncol(input.data),
+      function(j) {
+        predicted = as.numeric(
+          apply(ref.data, 2, function(i) {
+            cor(as.numeric(i), as.numeric(input.data[, j]), method = "spearman", use="complete.obs")
+          })
+        )
+        return(predicted)
+      }, mc.cores = 10
+    )
+
+    predicted.cell = do.call(cbind, predicted.cell)
+    rownames(predicted.cell) = colnames(ref.data)
+
+    ct = apply(predicted.cell, 2, function(x) {
+      return(as.numeric(which(rank(-x) <=5)))
+    }, simplify = F)
+
+    predicted.cell = pbmclapply(
+      1:ncol(input.data), function(i) {
+        ref = ref.data[,ct[[i]]]
+        g = which(rank(-rowVars(as.matrix(ref))) <= 2000)
+        ref = ref[g,]
+        input = input.data[g,i]
+        predict = apply(ref, 2, function(i) {
+          cor(as.numeric(i), input, method = "spearman", use="complete.obs")
+        })
+        return(c(names(sort(predict, decreasing = T)[1:2]), as.numeric(sort(predict, decreasing = T)[1:2])))
+      }, mc.cores = 10
+    )
+
+    predicted.cell = do.call(rbind, predicted.cell)
+    predicted.cell[,3] = round(as.numeric(predicted.cell[,3]), 3)
+    predicted.cell[,4] = round(as.numeric(predicted.cell[,4]), 3)
+    return(predicted.cell)
+  }
+}
+

README.md

@@ -4,6 +4,9 @@ FastIntegration is a fast and high-capacity version of Seurat Integration. FastI
 
 **Recent update: New functions which allow users to filter and download data in DISCO (<https://www.immunesinglecell.org/repository>), comprising 5200+ single-cell samples!**
 
+More vignettes can be found at https://immunesinglecell.org/vignette/docs/FastIntegration/cell-type-atlas
+
+
 ## Requirement
 
 FastIntegration requires the following packages: