1. singleCellTK
  2. man
  3. runDoubletFinder.Rd
Browse code

addressed do.call issue

mingl1997 authored on 07/01/2025 15:59:57
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ a57001ec
... ... 
@@ -12,6 +12,7 @@ runDoubletFinder(
12 12 
   seuratNfeatures = 2000,
13 13 
   seuratPcs = seq(15),
14 14 
   seuratRes = 1.5,
15 
+  sct = FALSE,
15 16 
   formationRate = 0.075,
16 17 
   nCores = NULL,
17 18 
   verbose = FALSE
... ... 
@@ -39,6 +40,8 @@ determine number of clusters. Default \code{1:15}.}
39 40 
 which adjusts the number of clusters determined via the algorithm. Default
40 41 
 \code{1.5}.}
41 42
43 
+\item{sct}{Whether or not to use SCT. Default \code{FALSE}.}
44 
+
42 45 
 \item{formationRate}{Doublet formation rate used within algorithm. Default
43 46 
 \code{0.075}.}
44 47
Browse code

fixed some more documentation errors

Ming Liu authored on 28/08/2024 19:59:36
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ 2ae06c9f
... ... 
@@ -58,6 +58,7 @@ Uses doubletFinder to determine cells within the dataset
58 58 
 }
59 59 
 \examples{
60 60 
 data(scExample, package = "singleCellTK")
61 
+options(future.globals.maxSize = 786432000)
61 62 
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
62 63 
 sce <- runDoubletFinder(sce)
63 64 
 }
Browse code

Update DoubletFinder

Yichen Wang authored on 14/10/2022 07:23:28
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ c97e881e
... ... 
@@ -6,8 +6,8 @@
6 6 
 \usage{
7 7 
 runDoubletFinder(
8 8 
   inSCE,
9 
-  useAssay = "counts",
10 9 
   sample = NULL,
10 
+  useAssay = "counts",
11 11 
   seed = 12345,
12 12 
   seuratNfeatures = 2000,
13 13 
   seuratPcs = seq(15),
... ... 
@@ -18,35 +18,39 @@ runDoubletFinder(
18 18 
 )
19 19 
 }
20 20 
 \arguments{
21 
-\item{inSCE}{Input SingleCellExperiment object. Must contain a counts matrix}
21 
+\item{inSCE}{inSCE A \linkS4class{SingleCellExperiment} object.}
22 22
23 
-\item{useAssay}{Indicate which assay to use. Default "counts".}
23 
+\item{sample}{Character vector or colData variable name. Indicates which
24 
+sample each cell belongs to. Default \code{NULL}.}
24 25
25 
-\item{sample}{Numeric vector. Each cell will be assigned a sample number.}
26 
+\item{useAssay}{A string specifying which assay in the SCE to use. Default
27 
+\code{"counts"}.}
26 28
27 
-\item{seed}{Seed for the random number generator. Default 12345.}
29 
+\item{seed}{Seed for the random number generator, can be set to \code{NULL}.
30 
+Default \code{12345}.}
28 31
29 32 
 \item{seuratNfeatures}{Integer. Number of highly variable genes to use.
30 
-Default 2000.}
33 
+Default \code{2000}.}
31 34
32 35 
 \item{seuratPcs}{Numeric vector. The PCs used in seurat function to
33 
-determine number of clusters. Default 1:15.}
36 
+determine number of clusters. Default \code{1:15}.}
34 37
35 
-\item{seuratRes}{Numeric vector. The resolution parameter used in seurat,
36 
-which adjusts the number of clusters determined via the algorithm.
37 
-Default 1.5.}
38 
+\item{seuratRes}{Numeric vector. The resolution parameter used in Seurat,
39 
+which adjusts the number of clusters determined via the algorithm. Default
40 
+\code{1.5}.}
38 41
39 
-\item{formationRate}{Doublet formation rate used within algorithm.
40 
-Default 0.075.}
42 
+\item{formationRate}{Doublet formation rate used within algorithm. Default
43 
+\code{0.075}.}
41 44
42 
-\item{nCores}{Number of cores used for running the function.}
45 
+\item{nCores}{Number of cores used for running the function. Default
46 
+\code{NULL}.}
43 47
44 
-\item{verbose}{Boolean. Wheter to print messages from Seurat and
45 
-DoubletFinder. Default FALSE.}
48 
+\item{verbose}{Boolean. Wheter to print messages from Seurat and
49 
+DoubletFinder. Default \code{FALSE}.}
46 50 
 }
47 51 
 \value{
48 
-SingleCellExperiment object containing the
49 
- 'doublet_finder_doublet_score'.
52 
+\linkS4class{SingleCellExperiment} object containing the
53 
+\code{doublet_finder_doublet_score} variable in \code{colData} slot.
50 54 
 }
51 55 
 \description{
52 56 
 Uses doubletFinder to determine cells within the dataset
... ... 
@@ -57,3 +61,6 @@ data(scExample, package = "singleCellTK")
57 61 
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
58 62 
 sce <- runDoubletFinder(sce)
59 63 
 }
64 
+\seealso{
65 
+\code{\link{runCellQC}}, \code{\link{plotDoubletFinderResults}}
66 
+}
Browse code

Updates to fix BiocCheck warning

Irzam Sarfraz authored on 09/05/2021 13:18:39
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ 97437081
... ... 
@@ -10,7 +10,7 @@ runDoubletFinder(
10 10 
   sample = NULL,
11 11 
   seed = 12345,
12 12 
   seuratNfeatures = 2000,
13 
-  seuratPcs = 1:15,
13 
+  seuratPcs = seq(15),
14 14 
   seuratRes = 1.5,
15 15 
   formationRate = 0.075,
16 16 
   nCores = NULL,
Browse code

Use subsetSCECols to subset data in example

Yusuke Koga authored on 15/10/2020 17:11:54
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ c06bc73b
... ... 
@@ -54,6 +54,6 @@ Uses doubletFinder to determine cells within the dataset
54 54 
 }
55 55 
 \examples{
56 56 
 data(scExample, package = "singleCellTK")
57 
-sce <- sce[, colData(sce)$type != 'EmptyDroplet']
57 
+sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
58 58 
 sce <- runDoubletFinder(sce)
59 59 
 }
Browse code

Add Runnable functions

Yusuke Koga authored on 15/10/2020 16:44:51
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ 0ccddee1
... ... 
@@ -53,9 +53,7 @@ Uses doubletFinder to determine cells within the dataset
53 53 
  suspected to be doublets.
54 54 
 }
55 55 
 \examples{
56 
-\donttest{
57 56 
 data(scExample, package = "singleCellTK")
58 57 
 sce <- sce[, colData(sce)$type != 'EmptyDroplet']
59 58 
 sce <- runDoubletFinder(sce)
60 59 
 }
61 
-}
Browse code

Minor updates to getPCA and seuratIntegration functions

irzamsarfraz authored on 10/07/2020 07:50:45
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ 8a70b39e
... ... 
@@ -53,7 +53,7 @@ Uses doubletFinder to determine cells within the dataset
53 53 
  suspected to be doublets.
54 54 
 }
55 55 
 \examples{
56 
-\dontrun{
56 
+\donttest{
57 57 
 data(scExample, package = "singleCellTK")
58 58 
 sce <- sce[, colData(sce)$type != 'EmptyDroplet']
59 59 
 sce <- runDoubletFinder(sce)
Browse code

Merge from upstream. Fix conflict of runQC.R and doubletFinder

rz2333 authored on 06/07/2020 02:04:19
Showing 0 changed files
Browse code

Update doubletFinder and SCTK_runQC.R

rz2333 authored on 06/07/2020 01:40:51
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ 505b7521
... ... 
@@ -43,8 +43,6 @@ Default 0.075.}
43 43 
 Default FALSE.}
44 44
45 45 
 \item{numCores}{Integer. Number of cores used to run doubletFinder. Default is 1 (no parallel computing).}
46 
-
47 
-\item{seed.}{Integer. Random seed set for computation. Default is 12345.}
48 46 
 }
49 47 
 \value{
50 48 
 SingleCellExperiment object containing the
Browse code

Finished fixing up importGeneSet functions. Modified and moved featureIndex function from Celda to sctk. Added msigdb object and documentation

Joshua D. Campbell authored on 28/06/2020 19:18:31
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ 70873af9
... ... 
@@ -53,7 +53,7 @@ Uses doubletFinder to determine cells within the dataset
53 53 
  suspected to be doublets.
54 54 
 }
55 55 
 \examples{
56 
-\dontrun{
56 
+\donttest{
57 57 
 data(scExample, package = "singleCellTK")
58 58 
 sce <- runDoubletFinder(sce)
59 59 
 }
Browse code

Update QC pipeline to support parallel computing

rz2333 authored on 23/06/2020 23:27:49
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ 7e045a5d
... ... 
@@ -13,7 +13,8 @@ runDoubletFinder(
13 13 
   seuratPcs = 1:15,
14 14 
   seuratRes = 1.5,
15 15 
   formationRate = 0.075,
16 
-  verbose = FALSE
16 
+  verbose = FALSE,
17 
+  numCores = 1
17 18 
 )
18 19 
 }
19 20 
 \arguments{
... ... 
@@ -40,6 +41,10 @@ Default 0.075.}
40 41
41 42 
 \item{verbose}{Boolean. Wheter to print messages from Seurat and DoubletFinder.
42 43 
 Default FALSE.}
44 
+
45 
+\item{numCores}{Integer. Number of cores used to run doubletFinder. Default is 1 (no parallel computing).}
46 
+
47 
+\item{seed.}{Integer. Random seed set for computation. Default is 12345.}
43 48 
 }
44 49 
 \value{
45 50 
 SingleCellExperiment object containing the
Browse code

Merge branch 'compbiomed-devel' into devel

rz2333 authored on 23/06/2020 14:41:31
Showing 0 changed files
Browse code

Update sctk qc pipeline to allow only droplet or cell input

rz2333 authored on 22/06/2020 17:48:28
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ 46357f0d
... ... 
@@ -52,6 +52,7 @@ Uses doubletFinder to determine cells within the dataset
52 52 
 \examples{
53 53 
 \dontrun{
54 54 
 data(scExample, package = "singleCellTK")
55 
+sce <- sce[, colData(sce)$type != 'EmptyDroplet']
55 56 
 sce <- runDoubletFinder(sce)
56 57 
 }
57 58 
 }
Browse code

Edit renv.lock temporarily

Yusuke Koga authored on 22/06/2020 15:02:33
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ 51bc585d
... ... 
@@ -13,6 +13,7 @@ runDoubletFinder(
13 13 
   seuratPcs = 1:15,
14 14 
   seuratRes = 1.5,
15 15 
   formationRate = 0.075,
16 
+  nCores = NULL,
16 17 
   verbose = FALSE
17 18 
 )
18 19 
 }
... ... 
@@ -38,8 +39,10 @@ Default 1.5.}
38 39 
 \item{formationRate}{Doublet formation rate used within algorithm.
39 40 
 Default 0.075.}
40 41
41 
-\item{verbose}{Boolean. Wheter to print messages from Seurat and DoubletFinder.
42 
-Default FALSE.}
42 
+\item{nCores}{Number of cores used for running the function.}
43 
+
44 
+\item{verbose}{Boolean. Wheter to print messages from Seurat and
45 
+DoubletFinder. Default FALSE.}
43 46 
 }
44 47 
 \value{
45 48 
 SingleCellExperiment object containing the
Browse code

Incorporate new per-QC plotting fxn

Yusuke Koga authored on 17/06/2020 13:39:12
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ bc6984ea
... ... 
@@ -11,7 +11,7 @@ runDoubletFinder(
11 11 
   seed = 12345,
12 12 
   seuratNfeatures = 2000,
13 13 
   seuratPcs = 1:15,
14 
-  seuratRes = c(0.5, 1, 1.5, 2),
14 
+  seuratRes = 1.5,
15 15 
   formationRate = 0.075,
16 16 
   verbose = FALSE
17 17 
 )
... ... 
@@ -33,7 +33,7 @@ determine number of clusters. Default 1:15.}
33 33
34 34 
 \item{seuratRes}{Numeric vector. The resolution parameter used in seurat,
35 35 
 which adjusts the number of clusters determined via the algorithm.
36 
-Default c(0.5, 1, 1.5, 2).}
36 
+Default 1.5.}
37 37
38 38 
 \item{formationRate}{Doublet formation rate used within algorithm.
39 39 
 Default 0.075.}
Browse code

update hemlReports.R and update example code in QC functions

rz2333 authored on 11/06/2020 19:29:13
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ 4991c249
... ... 
@@ -51,7 +51,7 @@ Uses doubletFinder to determine cells within the dataset
51 51 
 }
52 52 
 \examples{
53 53 
 \dontrun{
54 
-data(sceQCExample, package = "singleCellTK")
54 
+data(scExample, package = "singleCellTK")
55 55 
 sce <- runDoubletFinder(sce)
56 56 
 }
57 57 
 }
Browse code

Modifications to ggScatter, add bin fxn

Yusuke Koga authored on 24/05/2020 02:08:55
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ cc57a72f
... ... 
@@ -25,17 +25,21 @@ runDoubletFinder(
25 25
26 26 
 \item{seed}{Seed for the random number generator. Default 12345.}
27 27
28 
-\item{seuratNfeatures}{Integer. Number of highly variable genes to use. Default 2000.}
28 
+\item{seuratNfeatures}{Integer. Number of highly variable genes to use.
29 
+Default 2000.}
29 30
30 31 
 \item{seuratPcs}{Numeric vector. The PCs used in seurat function to
31 32 
 determine number of clusters. Default 1:15.}
32 33
33 
-\item{seuratRes}{Numeric vector. The resolution parameter used in seurat, which adjusts the
34 
-number of clusters determined via the algorithm. Default c(0.5, 1, 1.5, 2).}
34 
+\item{seuratRes}{Numeric vector. The resolution parameter used in seurat,
35 
+which adjusts the number of clusters determined via the algorithm.
36 
+Default c(0.5, 1, 1.5, 2).}
35 37
36 
-\item{formationRate}{Doublet formation rate used within algorithm. Default 0.075.}
38 
+\item{formationRate}{Doublet formation rate used within algorithm.
39 
+Default 0.075.}
37 40
38 
-\item{verbose}{Boolean. Wheter to print messages from Seurat and DoubletFinder. Default FALSE.}
41 
+\item{verbose}{Boolean. Wheter to print messages from Seurat and DoubletFinder.
42 
+Default FALSE.}
39 43 
 }
40 44 
 \value{
41 45 
 SingleCellExperiment object containing the
Browse code

Add new example data and HTAN meta export in QC pipeline

rz2333 authored on 18/05/2020 16:15:26
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ 6357ced6
... ... 
@@ -47,7 +47,7 @@ Uses doubletFinder to determine cells within the dataset
47 47 
 }
48 48 
 \examples{
49 49 
 \dontrun{
50 
-data(sce_chcl, package = "scds")
51 
-sce <- runDoubletFinder(sce_chcl)
50 
+data(sceQCExample, package = "singleCellTK")
51 
+sce <- runDoubletFinder(sce)
52 52 
 }
53 53 
 }
Browse code

Updated LIGER function and put correct dependencies in DESCRIPTION. Updated docs

Joshua D. Campbell authored on 06/03/2020 05:15:13
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ 64d3a71f
... ... 
@@ -4,10 +4,17 @@
4 4 
 \alias{runDoubletFinder}
5 5 
 \title{Generates a doublet score for each cell via doubletFinder}
6 6 
 \usage{
7 
-runDoubletFinder(inSCE, useAssay = "counts", sample = NULL,
8 
-  seed = 12345, seuratNfeatures = 2000, seuratPcs = 1:15,
9 
-  seuratRes = c(0.5, 1, 1.5, 2), formationRate = 0.075,
10 
-  verbose = FALSE)
7 
+runDoubletFinder(
8 
+  inSCE,
9 
+  useAssay = "counts",
10 
+  sample = NULL,
11 
+  seed = 12345,
12 
+  seuratNfeatures = 2000,
13 
+  seuratPcs = 1:15,
14 
+  seuratRes = c(0.5, 1, 1.5, 2),
15 
+  formationRate = 0.075,
16 
+  verbose = FALSE
17 
+)
11 18 
 }
12 19 
 \arguments{
13 20 
 \item{inSCE}{Input SingleCellExperiment object. Must contain a counts matrix}
Browse code

move to branch

Yichen Wang authored on 04/03/2020 20:32:17
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ e624033d
... ... 
@@ -4,17 +4,10 @@
4 4 
 \alias{runDoubletFinder}
5 5 
 \title{Generates a doublet score for each cell via doubletFinder}
6 6 
 \usage{
7 
-runDoubletFinder(
8 
-  inSCE,
9 
-  useAssay = "counts",
10 
-  sample = NULL,
11 
-  seed = 12345,
12 
-  seuratNfeatures = 2000,
13 
-  seuratPcs = 1:15,
14 
-  seuratRes = c(0.5, 1, 1.5, 2),
15 
-  formationRate = 0.075,
16 
-  verbose = FALSE
17 
-)
7 
+runDoubletFinder(inSCE, useAssay = "counts", sample = NULL,
8 
+  seed = 12345, seuratNfeatures = 2000, seuratPcs = 1:15,
9 
+  seuratRes = c(0.5, 1, 1.5, 2), formationRate = 0.075,
10 
+  verbose = FALSE)
18 11 
 }
19 12 
 \arguments{
20 13 
 \item{inSCE}{Input SingleCellExperiment object. Must contain a counts matrix}
Browse code

update docs

zhewa authored on 24/02/2020 07:07:13
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ cdc5bdf4
... ... 
@@ -4,10 +4,17 @@
4 4 
 \alias{runDoubletFinder}
5 5 
 \title{Generates a doublet score for each cell via doubletFinder}
6 6 
 \usage{
7 
-runDoubletFinder(inSCE, useAssay = "counts", sample = NULL,
8 
-  seed = 12345, seuratNfeatures = 2000, seuratPcs = 1:15,
9 
-  seuratRes = c(0.5, 1, 1.5, 2), formationRate = 0.075,
10 
-  verbose = FALSE)
7 
+runDoubletFinder(
8 
+  inSCE,
9 
+  useAssay = "counts",
10 
+  sample = NULL,
11 
+  seed = 12345,
12 
+  seuratNfeatures = 2000,
13 
+  seuratPcs = 1:15,
14 
+  seuratRes = c(0.5, 1, 1.5, 2),
15 
+  formationRate = 0.075,
16 
+  verbose = FALSE
17 
+)
11 18 
 }
12 19 
 \arguments{
13 20 
 \item{inSCE}{Input SingleCellExperiment object. Must contain a counts matrix}
Browse code

Merge branch 'importQC' of github.com:ykoga07/singleCellTK into importQC

zhewa authored on 24/02/2020 06:37:54
Showing 0 changed files
Browse code

Made new utility funciton for converting to dgCMatrix and not losing dimnames (as would happen if the matrix was wrapped in delayed array). Updated all conversion code to use this function. Updated documentation. Fixed one bug in 'runCxdsBcdsHybrid'

Joshua D. Campbell authored on 24/02/2020 02:41:26
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ fef86099
... ... 
@@ -40,6 +40,8 @@ Uses doubletFinder to determine cells within the dataset
40 40 
  suspected to be doublets.
41 41 
 }
42 42 
 \examples{
43 
+\dontrun{
43 44 
 data(sce_chcl, package = "scds")
44 45 
 sce <- runDoubletFinder(sce_chcl)
45 46 
 }
47 
+}
Browse code

Debug doubletFinder, modify README

Yusuke Koga authored on 22/02/2020 17:07:09
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ 82457c5c
... ... 
@@ -4,23 +4,29 @@
4 4 
 \alias{runDoubletFinder}
5 5 
 \title{Generates a doublet score for each cell via doubletFinder}
6 6 
 \usage{
7 
-runDoubletFinder(sce, sample = NULL, seed = 12345, seurat.pcs = 1:15,
8 
-  seurat.res = 2, seurat.nfeatures = 2000, verbose = FALSE)
7 
+runDoubletFinder(inSCE, useAssay = "counts", sample = NULL,
8 
+  seed = 12345, seuratNfeatures = 2000, seuratPcs = 1:15,
9 
+  seuratRes = c(0.5, 1, 1.5, 2), formationRate = 0.075,
10 
+  verbose = FALSE)
9 11 
 }
10 12 
 \arguments{
11 
-\item{sce}{SingleCellExperiment object. Must contain a counts matrix}
13 
+\item{inSCE}{Input SingleCellExperiment object. Must contain a counts matrix}
14 
+
15 
+\item{useAssay}{Indicate which assay to use. Default "counts".}
12 16
13 17 
 \item{sample}{Numeric vector. Each cell will be assigned a sample number.}
14 18
15 19 
 \item{seed}{Seed for the random number generator. Default 12345.}
16 20
17 
-\item{seurat.pcs}{Numeric vector. The PCs used in seurat function to
21 
+\item{seuratNfeatures}{Integer. Number of highly variable genes to use. Default 2000.}
22 
+
23 
+\item{seuratPcs}{Numeric vector. The PCs used in seurat function to
18 24 
 determine number of clusters. Default 1:15.}
19 25
20 
-\item{seurat.res}{Numeric vector. The resolution parameter used in seurat
21 
-which adjusts the number of clusters determined via the algorithm. Default 2.}
26 
+\item{seuratRes}{Numeric vector. The resolution parameter used in seurat, which adjusts the
27 
+number of clusters determined via the algorithm. Default c(0.5, 1, 1.5, 2).}
22 28
23 
-\item{seurat.nfeatures}{Integer. Number of highly variable genes to use. Default 2000.}
29 
+\item{formationRate}{Doublet formation rate used within algorithm. Default 0.075.}
24 30
25 31 
 \item{verbose}{Boolean. Wheter to print messages from Seurat and DoubletFinder. Default FALSE.}
26 32 
 }
Browse code

Add outputs table to README

Yusuke Koga authored on 20/02/2020 20:07:41
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ 422d4ca9
... ... 
@@ -4,15 +4,8 @@
4 4 
 \alias{runDoubletFinder}
5 5 
 \title{Generates a doublet score for each cell via doubletFinder}
6 6 
 \usage{
7 
-runDoubletFinder(
8 
-  sce,
9 
-  sample = NULL,
10 
-  seed = 12345,
11 
-  seurat.pcs = 1:15,
12 
-  seurat.res = 2,
13 
-  seurat.nfeatures = 2000,
14 
-  verbose = FALSE
15 
-)
7 
+runDoubletFinder(sce, sample = NULL, seed = 12345, seurat.pcs = 1:15,
8 
+  seurat.res = 2, seurat.nfeatures = 2000, verbose = FALSE)
16 9 
 }
17 10 
 \arguments{
18 11 
 \item{sce}{SingleCellExperiment object. Must contain a counts matrix}
Browse code

Fixed examples

Joshua D. Campbell authored on 15/02/2020 01:03:26
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ b3ed78d5
... ... 
@@ -40,5 +40,6 @@ Uses doubletFinder to determine cells within the dataset
40 40 
  suspected to be doublets.
41 41 
 }
42 42 
 \examples{
43 
-sce <- runDoubletFinder(sce)
43 
+data(sce_chcl, package = "scds")
44 
+sce <- runDoubletFinder(sce_chcl)
44 45 
 }
Browse code

Fixed errors/warnings in DoubletFinder code. Updated docs. Added documentation for importCellRangerV2/V3Sample functions. Added install of DoubletFinder from github in DESCRIPTION and in .travis.yml

Joshua D. Campbell authored on 15/02/2020 00:05:10
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ 8a33a64b
... ... 
@@ -4,8 +4,15 @@
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 \alias{runDoubletFinder}
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 \title{Generates a doublet score for each cell via doubletFinder}
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 \usage{
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-runDoubletFinder(sce, sample, seed = 12345, seurat.pcs = 1:15,
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-  seurat.res = 1.2, ...)
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+runDoubletFinder(
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+  sce,
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+  sample = NULL,
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+  seed = 12345,
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+  seurat.pcs = 1:15,
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+  seurat.res = 2,
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+  seurat.nfeatures = 2000,
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+  verbose = FALSE
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+)
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 }
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 \arguments{
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 \item{sce}{SingleCellExperiment object. Must contain a counts matrix}
... ... 
@@ -18,7 +25,11 @@ runDoubletFinder(sce, sample, seed = 12345, seurat.pcs = 1:15,
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 determine number of clusters. Default 1:15.}
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 \item{seurat.res}{Numeric vector. The resolution parameter used in seurat
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-which adjusts the number of clusters determined via the algorithm. Default 1.2.}
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+which adjusts the number of clusters determined via the algorithm. Default 2.}
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+
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+\item{seurat.nfeatures}{Integer. Number of highly variable genes to use. Default 2000.}
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+
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+\item{verbose}{Boolean. Wheter to print messages from Seurat and DoubletFinder. Default FALSE.}
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 }
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 \value{
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 SingleCellExperiment object containing the
Browse code

Modifications to doubletFinder

Yusuke Koga authored on 13/02/2020 04:24:15
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ 39f89f1f
... ... 
@@ -4,7 +4,8 @@
4 4 
 \alias{runDoubletFinder}
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 \title{Generates a doublet score for each cell via doubletFinder}
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 \usage{
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-runDoubletFinder(sce, sample, seed = 12345, ...)
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+runDoubletFinder(sce, sample, seed = 12345, seurat.pcs = 1:15,
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+  seurat.res = 1.2, ...)
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 }
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 \arguments{
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 \item{sce}{SingleCellExperiment object. Must contain a counts matrix}
... ... 
@@ -12,6 +13,12 @@ runDoubletFinder(sce, sample, seed = 12345, ...)
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 \item{sample}{Numeric vector. Each cell will be assigned a sample number.}
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 \item{seed}{Seed for the random number generator. Default 12345.}
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+
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+\item{seurat.pcs}{Numeric vector. The PCs used in seurat function to
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+determine number of clusters. Default 1:15.}
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+
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+\item{seurat.res}{Numeric vector. The resolution parameter used in seurat
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+which adjusts the number of clusters determined via the algorithm. Default 1.2.}
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 }
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 \value{
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 SingleCellExperiment object containing the
Browse code

Re-add doubletFinder, modify runQC.R and SCTK_runQC.R pipeline to accomodate doubletFinder

Yusuke Koga authored on 24/01/2020 17:48:52
Showing 1 changed files
man/runDoubletFinder.Rd
History View file @ 6bb2492f
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,26 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/doubletFinder_doubletDetection.R
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+\name{runDoubletFinder}
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+\alias{runDoubletFinder}
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+\title{Generates a doublet score for each cell via doubletFinder}
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+\usage{
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+runDoubletFinder(sce, sample, seed = 12345, ...)
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+}
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+\arguments{
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+\item{sce}{SingleCellExperiment object. Must contain a counts matrix}
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+
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+\item{sample}{Numeric vector. Each cell will be assigned a sample number.}
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+
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+\item{seed}{Seed for the random number generator. Default 12345.}
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+}
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+\value{
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+SingleCellExperiment object containing the
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+ 'doublet_finder_doublet_score'.
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+}
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+\description{
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+Uses doubletFinder to determine cells within the dataset
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+ suspected to be doublets.
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+}
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+\examples{
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+sce <- runDoubletFinder(sce)
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+}