Modify code

.Rproj.user/D2E2BE0D/pcs/files-pane.pper

@@ -1,5 +1,5 @@
 {
-    "path" : "~/Documents/FBT/Single/package/GapClust",
+    "path" : "~/Documents/FBT/Single/package/GapClust/man",
     "sortOrder" : [
         {
             "ascending" : true,

.Rproj.user/D2E2BE0D/pcs/workbench-pane.pper

@@ -1,6 +1,6 @@
 {
     "TabSet1" : 3,
-    "TabSet2" : 1,
+    "TabSet2" : 0,
     "TabZoom" : {
     }
 }

.Rproj.user/D2E2BE0D/persistent-state

@@ -1,8 +1,8 @@
 build-last-errors="[]"
 build-last-errors-base-dir="~/Documents/FBT/Single/package/GapClust/"
-build-last-outputs="[{\"output\":\"==> R CMD INSTALL --no-multiarch --with-keep.source GapClust\\n\\n\",\"type\":0},{\"output\":\"* installing to library ‘/home/sam/R/x86_64-pc-linux-gnu-library/3.6’\\n\",\"type\":1},{\"output\":\"* installing *source* package ‘GapClust’ ...\\n\",\"type\":1},{\"output\":\"** using staged installation\\n\",\"type\":1},{\"output\":\"** R\\n\",\"type\":1},{\"output\":\"** byte-compile and prepare package for lazy loading\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** help\\n\",\"type\":1},{\"output\":\"*** installing help indices\\n\",\"type\":1},{\"output\":\"** building package indices\\n\",\"type\":1},{\"output\":\"** testing if installed package can be loaded from temporary location\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** testing if installed package can be loaded from final location\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** testing if installed package keeps a record of temporary installation path\\n\",\"type\":1},{\"output\":\"* DONE (GapClust)\\n\",\"type\":1},{\"output\":\"\",\"type\":1}]"
+build-last-outputs="[{\"output\":\"==> R CMD INSTALL --no-multiarch --with-keep.source GapClust\\n\\n\",\"type\":0},{\"output\":\"* installing to library ‘/home/sam/R/x86_64-pc-linux-gnu-library/3.6’\\n\",\"type\":1},{\"output\":\"* installing *source* package ‘GapClust’ ...\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** using staged installation\\n\",\"type\":1},{\"output\":\"** R\\n\",\"type\":1},{\"output\":\"** byte-compile and prepare package for lazy loading\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** help\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"*** installing help indices\\n\",\"type\":1},{\"output\":\"** building package indices\\n\",\"type\":1},{\"output\":\"** testing if installed package can be loaded from temporary location\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** testing if installed package can be loaded from final location\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** testing if installed package keeps a record of temporary installation path\\n\",\"type\":1},{\"output\":\"* DONE (GapClust)\\n\",\"type\":1},{\"output\":\"\",\"type\":1}]"
 compile_pdf_state="{\"errors\":[],\"output\":\"\",\"running\":false,\"tab_visible\":false,\"target_file\":\"\"}"
 files.monitored-path=""
 find-in-files-state="{\"handle\":\"\",\"input\":\"\",\"path\":\"\",\"regex\":true,\"results\":{\"file\":[],\"line\":[],\"lineValue\":[],\"matchOff\":[],\"matchOn\":[]},\"running\":false}"
-imageDirtyState="1"
-saveActionState="-1"
+imageDirtyState="0"
+saveActionState="0"

.Rproj.user/D2E2BE0D/sources/prop/6C59A91

@@ -1,4 +1,4 @@
 {
-    "cursorPosition" : "100,0",
-    "scrollLine" : "81"
+    "cursorPosition" : "90,64",
+    "scrollLine" : "77"
 }

.Rproj.user/D2E2BE0D/sources/prop/CFC898F2

@@ -0,0 +1,4 @@
+{
+    "cursorPosition" : "7,122",
+    "scrollLine" : "0"
+}

.Rproj.user/D2E2BE0D/sources/prop/INDEX

@@ -2,6 +2,7 @@
 ~%2FDocuments%2FFBT%2FSingle%2Fpackage%2FGapClust%2FDESCRIPTION="51B67C04"
 ~%2FDocuments%2FFBT%2FSingle%2Fpackage%2FGapClust%2FNAMESPACE="5DA31145"
 ~%2FDocuments%2FFBT%2FSingle%2Fpackage%2FGapClust%2FR%2FGapClust.R="6C59A91"
+~%2FDocuments%2FFBT%2FSingle%2Fpackage%2FGapClust%2Fman%2FGapClust.Rd="CFC898F2"
 ~%2FDocuments%2FFBT%2FSingle%2Fpackage%2FGapClust_manuscript%2FRscript%2FALL_10X_doublets.R="65DF4126"
 ~%2FDocuments%2FFBT%2FSingle%2Fpackage%2Fminerva_1.5.8%2FGapClust%2FGapClust%2FDESCRIPTION="F323D26F"
 ~%2FDocuments%2FFBT%2FSingle%2Fpackage%2Fminerva_1.5.8%2FGapClust%2FGapClust%2FNAMESPACE="18AAA614"

.Rproj.user/D2E2BE0D/sources/s-504B2FB1/8D9CCF8A → .Rproj.user/D2E2BE0D/sources/s-36E65813/8D9CCF8A

@@ -12,8 +12,8 @@
     "path" : "~/Documents/FBT/Single/package/GapClust/R/GapClust.R",
     "project_path" : "R/GapClust.R",
     "properties" : {
-        "cursorPosition" : "100,0",
-        "scrollLine" : "81"
+        "cursorPosition" : "90,64",
+        "scrollLine" : "77"
     },
     "relative_order" : 1,
     "source_on_save" : false,

.Rproj.user/D2E2BE0D/sources/s-36E65813/F5671F33-contents

@@ -0,0 +1,19 @@
+\name{GapClust}
+\alias{GapClust}
+\title{Detecting rare cells from expression profiles by single cell RNA-seq.}
+\usage{
+GapClust(data, k=200)
+}
+\arguments{
+  \item{data}{ a data matrix, normalized expression profiles of single cells, where rows are genes and columns are cells. }
+  \item{k}{ number of neighbors to consider and the upper limit of minor cluster size. }
+}
+\description{
+GapClust takes advantage of the gap between minor cluster and neighbouring
+abundant cluster to let rare cells within minor cluster stand out through
+delicately designed statistics. Meanwhile, GapClust does not struggle to
+search for rare cell informative genes like most of the competitors,
+but learns the cluster size as well as rare cells using simple arithmetic calculation.
+}
+\examples{
+}