chen.j@wehi.edu.au -
21 Mar 2024
- +22 Mar 2024
+ Source:vignettes/smartid_Demo.Rmd
smartid_Demo.RmdPrepare Data
-library(smartid)
+library(smartid)
library(SummarizedExperiment)
library(splatter)
library(ggplot2)
@@ -238,7 +245,7 @@ Score Samples)
)
#> user system elapsed
-#> 0.206 0.000 0.206
+#> 0.196 0.008 0.204
## score and tf,idf,iae all saved
assays(data_sim)
@@ -438,7 +445,7 @@ Score Samples )
)
#> user system elapsed
-#> 0.144 0.008 0.151
+#> 0.137 0.016 0.153
## new score is saved and tf,idf,iae all updated
assays(data_sim)
diff --git a/authors.html b/authors.html
index 54131c7..d8bb898 100644
--- a/authors.html
+++ b/authors.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -60,20 +66,21 @@ Authors
Citation
-
+ Source: DESCRIPTION
Chen J (2024).
smartid: Scoring and Marker Selection Method Based on Modified TF-IDF.
-R package version 0.99.1.
+R package version 0.99.1, https://davislaboratory.github.io/smartid.
@Manual{,
title = {smartid: Scoring and Marker Selection Method Based on Modified TF-IDF},
author = {Jinjin Chen},
year = {2024},
note = {R package version 0.99.1},
+ url = {https://davislaboratory.github.io/smartid},
}
diff --git a/index.html b/index.html
index 6fb915c..cf6eabf 100644
--- a/index.html
+++ b/index.html
@@ -62,7 +62,14 @@
Changelog
-
+
@@ -95,7 +102,15 @@ Installation
-
+
+Links
+
+
+
+
License
- Full license
diff --git a/news/index.html b/news/index.html
index cd22383..1ba1816 100644
--- a/news/index.html
+++ b/news/index.html
@@ -38,7 +38,13 @@
-
Changelog
-
+
@@ -48,7 +54,7 @@
Changelog
-
+ Source: NEWS.md
diff --git a/pkgdown.yml b/pkgdown.yml
index 4344474..a52eed5 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.7
pkgdown_sha: ~
articles:
smartid_Demo: smartid_Demo.html
-last_built: 2024-03-21T16:35Z
+last_built: 2024-03-22T03:56Z
diff --git a/reference/cal_score.html b/reference/cal_score.html
index e07020c..77b4033 100644
--- a/reference/cal_score.html
+++ b/reference/cal_score.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/cal_score_init.html b/reference/cal_score_init.html
index 2b9cf24..22d02b0 100644
--- a/reference/cal_score_init.html
+++ b/reference/cal_score_init.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/gs_score.html b/reference/gs_score.html
index 01f2cb4..15ebdfc 100644
--- a/reference/gs_score.html
+++ b/reference/gs_score.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
compute overall score based on the given marker list
-
+ Source: R/AllGenerics.R, R/gs_score-methods.R
gs_score.Rd
diff --git a/reference/gs_score_init.html b/reference/gs_score_init.html
index cbbdce2..8a4b2f5 100644
--- a/reference/gs_score_init.html
+++ b/reference/gs_score_init.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/iae.html b/reference/iae.html
index b2b3f95..32d10bd 100644
--- a/reference/iae.html
+++ b/reference/iae.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/iae_hdb.html b/reference/iae_hdb.html
index f063cc9..319972d 100644
--- a/reference/iae_hdb.html
+++ b/reference/iae_hdb.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
inverse average expression using hdbscan cluster as label
-
+ Source: R/tf_idf_iae_wrappers.R
iae_hdb.Rd
diff --git a/reference/iae_igm.html b/reference/iae_igm.html
index aec68a7..3fb167c 100644
--- a/reference/iae_igm.html
+++ b/reference/iae_igm.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/iae_m.html b/reference/iae_m.html
index 1ff3aa0..571ba0e 100644
--- a/reference/iae_m.html
+++ b/reference/iae_m.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/iae_prob.html b/reference/iae_prob.html
index cf9533e..41b1e1c 100644
--- a/reference/iae_prob.html
+++ b/reference/iae_prob.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
labeled inverse average expression: probability based
-
+ Source: R/tf_idf_iae_wrappers.R
iae_prob.Rd
diff --git a/reference/iae_rf.html b/reference/iae_rf.html
index 33abe9f..92b4327 100644
--- a/reference/iae_rf.html
+++ b/reference/iae_rf.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
labeled inverse average expression: relative frequency
-
+ Source: R/tf_idf_iae_wrappers.R
iae_rf.Rd
diff --git a/reference/iae_sd.html b/reference/iae_sd.html
index 4550ebe..83e4bd9 100644
--- a/reference/iae_sd.html
+++ b/reference/iae_sd.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
inverse average expression using standard deviation (SD)
-
+ Source: R/tf_idf_iae_wrappers.R
iae_sd.Rd
diff --git a/reference/idf.html b/reference/idf.html
index 6debca3..c0e4080 100644
--- a/reference/idf.html
+++ b/reference/idf.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/idf_hdb.html b/reference/idf_hdb.html
index 125928e..c240c77 100644
--- a/reference/idf_hdb.html
+++ b/reference/idf_hdb.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/idf_iae_methods.html b/reference/idf_iae_methods.html
index cddf97c..47f06c3 100644
--- a/reference/idf_iae_methods.html
+++ b/reference/idf_iae_methods.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/idf_igm.html b/reference/idf_igm.html
index b2ad417..343613a 100644
--- a/reference/idf_igm.html
+++ b/reference/idf_igm.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/idf_m.html b/reference/idf_m.html
index e4ce722..94cf424 100644
--- a/reference/idf_m.html
+++ b/reference/idf_m.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/idf_prob.html b/reference/idf_prob.html
index ec8bbab..6f885ef 100644
--- a/reference/idf_prob.html
+++ b/reference/idf_prob.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/idf_rf.html b/reference/idf_rf.html
index c2ee706..ccc282d 100644
--- a/reference/idf_rf.html
+++ b/reference/idf_rf.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/idf_sd.html b/reference/idf_sd.html
index 0b7bdf3..644008f 100644
--- a/reference/idf_sd.html
+++ b/reference/idf_sd.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/index.html b/reference/index.html
index 9436499..958eae5 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -38,7 +38,13 @@
Changelog
-
+
diff --git a/reference/markers_hdbscan.html b/reference/markers_hdbscan.html
index 7ee1daa..991bf42 100644
--- a/reference/markers_hdbscan.html
+++ b/reference/markers_hdbscan.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/markers_mclust.html b/reference/markers_mclust.html
index 8ffe893..df8ed08 100644
--- a/reference/markers_mclust.html
+++ b/reference/markers_mclust.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/markers_mixmdl.html b/reference/markers_mixmdl.html
index 4914787..ce3e16a 100644
--- a/reference/markers_mixmdl.html
+++ b/reference/markers_mixmdl.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/ova_score_boxplot.html b/reference/ova_score_boxplot.html
index b1ae916..630995d 100644
--- a/reference/ova_score_boxplot.html
+++ b/reference/ova_score_boxplot.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/scale_mgm.html b/reference/scale_mgm.html
index debb1e1..b6ebefe 100644
--- a/reference/scale_mgm.html
+++ b/reference/scale_mgm.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/score_barplot.html b/reference/score_barplot.html
index 7a0b548..7bd7d09 100644
--- a/reference/score_barplot.html
+++ b/reference/score_barplot.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/sim_sce_test.html b/reference/sim_sce_test.html
index 46cf413..c069778 100644
--- a/reference/sim_sce_test.html
+++ b/reference/sim_sce_test.html
@@ -39,7 +39,13 @@
Changelog
-
+
@@ -49,7 +55,7 @@
scRNA-seq test data of 4 groups simulated by splatter.
-
+ Source: R/smartid-package.R
sim_sce_test.Rd
diff --git a/reference/sin_score_boxplot.html b/reference/sin_score_boxplot.html
index 6582272..fce0e67 100644
--- a/reference/sin_score_boxplot.html
+++ b/reference/sin_score_boxplot.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
@@ -97,7 +103,8 @@ Examples
#> Warning: `add_rownames()` was deprecated in dplyr 1.0.0.
#> ℹ Please use `tibble::rownames_to_column()` instead.
#> ℹ The deprecated feature was likely used in the smartid package.
-#> Please report the issue to the authors.
+#> Please report the issue at
+#> <https://github.com/DavisLaboratory/smartid/issues>.
diff --git a/reference/smartid_Package.html b/reference/smartid_Package.html
index fc895a6..08259db 100644
--- a/reference/smartid_Package.html
+++ b/reference/smartid_Package.html
@@ -42,7 +42,13 @@
Changelog
-
+
@@ -52,7 +58,7 @@
Scoring and Marker Selection method based on modified TF-IDF
-
+ Source: R/smartid-package.R
smartid_Package.Rd
diff --git a/reference/tf.html b/reference/tf.html
index 071c0b9..65842e5 100644
--- a/reference/tf.html
+++ b/reference/tf.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/top_markers.html b/reference/top_markers.html
index e6a0295..c992dd3 100644
--- a/reference/top_markers.html
+++ b/reference/top_markers.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
scale score and return top markers
-
+ Source: R/AllGenerics.R, R/top_markers-methods.R
top_markers.Rd
diff --git a/reference/top_markers_abs.html b/reference/top_markers_abs.html
index 57d2ef1..625a3ef 100644
--- a/reference/top_markers_abs.html
+++ b/reference/top_markers_abs.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
calculate group median, MAD or mean score and order genes based on scores
-
+ Source: R/top_markers.R
top_markers_abs.Rd
diff --git a/reference/top_markers_glm.html b/reference/top_markers_glm.html
index 83d3700..f0f1854 100644
--- a/reference/top_markers_glm.html
+++ b/reference/top_markers_glm.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
calculate group mean score using glm and order genes based on scores difference
-
+ Source: R/top_markers.R
top_markers_glm.Rd
diff --git a/reference/top_markers_init.html b/reference/top_markers_init.html
index 64197e4..1a85152 100644
--- a/reference/top_markers_init.html
+++ b/reference/top_markers_init.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
compute group summarized score and order genes based on processed scores
-
+ Source: R/top_markers.R
top_markers_init.Rd
library(smartid)
+library(smartid)
library(SummarizedExperiment)
library(splatter)
library(ggplot2)
@@ -238,7 +245,7 @@ Score Samples)
)
#> user system elapsed
-#> 0.206 0.000 0.206
+#> 0.196 0.008 0.204
## score and tf,idf,iae all saved
assays(data_sim)
@@ -438,7 +445,7 @@ Score Samples )
)
#> user system elapsed
-#> 0.144 0.008 0.151
+#> 0.137 0.016 0.153
## new score is saved and tf,idf,iae all updated
assays(data_sim)
diff --git a/authors.html b/authors.html
index 54131c7..d8bb898 100644
--- a/authors.html
+++ b/authors.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -60,20 +66,21 @@ Authors
Citation
-
+ Source: DESCRIPTION
Chen J (2024).
smartid: Scoring and Marker Selection Method Based on Modified TF-IDF.
-R package version 0.99.1.
+R package version 0.99.1, https://davislaboratory.github.io/smartid.
@Manual{,
title = {smartid: Scoring and Marker Selection Method Based on Modified TF-IDF},
author = {Jinjin Chen},
year = {2024},
note = {R package version 0.99.1},
+ url = {https://davislaboratory.github.io/smartid},
}
diff --git a/index.html b/index.html
index 6fb915c..cf6eabf 100644
--- a/index.html
+++ b/index.html
@@ -62,7 +62,14 @@
Changelog
-
+
@@ -95,7 +102,15 @@ Installation
-
+
+Links
+
+
+
+
License
- Full license
diff --git a/news/index.html b/news/index.html
index cd22383..1ba1816 100644
--- a/news/index.html
+++ b/news/index.html
@@ -38,7 +38,13 @@
-
Changelog
-
+
@@ -48,7 +54,7 @@
Changelog
-
+ Source: NEWS.md
diff --git a/pkgdown.yml b/pkgdown.yml
index 4344474..a52eed5 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.7
pkgdown_sha: ~
articles:
smartid_Demo: smartid_Demo.html
-last_built: 2024-03-21T16:35Z
+last_built: 2024-03-22T03:56Z
diff --git a/reference/cal_score.html b/reference/cal_score.html
index e07020c..77b4033 100644
--- a/reference/cal_score.html
+++ b/reference/cal_score.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/cal_score_init.html b/reference/cal_score_init.html
index 2b9cf24..22d02b0 100644
--- a/reference/cal_score_init.html
+++ b/reference/cal_score_init.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/gs_score.html b/reference/gs_score.html
index 01f2cb4..15ebdfc 100644
--- a/reference/gs_score.html
+++ b/reference/gs_score.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
compute overall score based on the given marker list
-
+ Source: R/AllGenerics.R, R/gs_score-methods.R
gs_score.Rd
diff --git a/reference/gs_score_init.html b/reference/gs_score_init.html
index cbbdce2..8a4b2f5 100644
--- a/reference/gs_score_init.html
+++ b/reference/gs_score_init.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/iae.html b/reference/iae.html
index b2b3f95..32d10bd 100644
--- a/reference/iae.html
+++ b/reference/iae.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/iae_hdb.html b/reference/iae_hdb.html
index f063cc9..319972d 100644
--- a/reference/iae_hdb.html
+++ b/reference/iae_hdb.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
inverse average expression using hdbscan cluster as label
-
+ Source: R/tf_idf_iae_wrappers.R
iae_hdb.Rd
diff --git a/reference/iae_igm.html b/reference/iae_igm.html
index aec68a7..3fb167c 100644
--- a/reference/iae_igm.html
+++ b/reference/iae_igm.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/iae_m.html b/reference/iae_m.html
index 1ff3aa0..571ba0e 100644
--- a/reference/iae_m.html
+++ b/reference/iae_m.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/iae_prob.html b/reference/iae_prob.html
index cf9533e..41b1e1c 100644
--- a/reference/iae_prob.html
+++ b/reference/iae_prob.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
labeled inverse average expression: probability based
-
+ Source: R/tf_idf_iae_wrappers.R
iae_prob.Rd
diff --git a/reference/iae_rf.html b/reference/iae_rf.html
index 33abe9f..92b4327 100644
--- a/reference/iae_rf.html
+++ b/reference/iae_rf.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
labeled inverse average expression: relative frequency
-
+ Source: R/tf_idf_iae_wrappers.R
iae_rf.Rd
diff --git a/reference/iae_sd.html b/reference/iae_sd.html
index 4550ebe..83e4bd9 100644
--- a/reference/iae_sd.html
+++ b/reference/iae_sd.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
inverse average expression using standard deviation (SD)
-
+ Source: R/tf_idf_iae_wrappers.R
iae_sd.Rd
diff --git a/reference/idf.html b/reference/idf.html
index 6debca3..c0e4080 100644
--- a/reference/idf.html
+++ b/reference/idf.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/idf_hdb.html b/reference/idf_hdb.html
index 125928e..c240c77 100644
--- a/reference/idf_hdb.html
+++ b/reference/idf_hdb.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/idf_iae_methods.html b/reference/idf_iae_methods.html
index cddf97c..47f06c3 100644
--- a/reference/idf_iae_methods.html
+++ b/reference/idf_iae_methods.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/idf_igm.html b/reference/idf_igm.html
index b2ad417..343613a 100644
--- a/reference/idf_igm.html
+++ b/reference/idf_igm.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/idf_m.html b/reference/idf_m.html
index e4ce722..94cf424 100644
--- a/reference/idf_m.html
+++ b/reference/idf_m.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/idf_prob.html b/reference/idf_prob.html
index ec8bbab..6f885ef 100644
--- a/reference/idf_prob.html
+++ b/reference/idf_prob.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/idf_rf.html b/reference/idf_rf.html
index c2ee706..ccc282d 100644
--- a/reference/idf_rf.html
+++ b/reference/idf_rf.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/idf_sd.html b/reference/idf_sd.html
index 0b7bdf3..644008f 100644
--- a/reference/idf_sd.html
+++ b/reference/idf_sd.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/index.html b/reference/index.html
index 9436499..958eae5 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -38,7 +38,13 @@
Changelog
-
+
diff --git a/reference/markers_hdbscan.html b/reference/markers_hdbscan.html
index 7ee1daa..991bf42 100644
--- a/reference/markers_hdbscan.html
+++ b/reference/markers_hdbscan.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/markers_mclust.html b/reference/markers_mclust.html
index 8ffe893..df8ed08 100644
--- a/reference/markers_mclust.html
+++ b/reference/markers_mclust.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/markers_mixmdl.html b/reference/markers_mixmdl.html
index 4914787..ce3e16a 100644
--- a/reference/markers_mixmdl.html
+++ b/reference/markers_mixmdl.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/ova_score_boxplot.html b/reference/ova_score_boxplot.html
index b1ae916..630995d 100644
--- a/reference/ova_score_boxplot.html
+++ b/reference/ova_score_boxplot.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/scale_mgm.html b/reference/scale_mgm.html
index debb1e1..b6ebefe 100644
--- a/reference/scale_mgm.html
+++ b/reference/scale_mgm.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/score_barplot.html b/reference/score_barplot.html
index 7a0b548..7bd7d09 100644
--- a/reference/score_barplot.html
+++ b/reference/score_barplot.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/sim_sce_test.html b/reference/sim_sce_test.html
index 46cf413..c069778 100644
--- a/reference/sim_sce_test.html
+++ b/reference/sim_sce_test.html
@@ -39,7 +39,13 @@
Changelog
-
+
@@ -49,7 +55,7 @@
scRNA-seq test data of 4 groups simulated by splatter.
-
+ Source: R/smartid-package.R
sim_sce_test.Rd
diff --git a/reference/sin_score_boxplot.html b/reference/sin_score_boxplot.html
index 6582272..fce0e67 100644
--- a/reference/sin_score_boxplot.html
+++ b/reference/sin_score_boxplot.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
@@ -97,7 +103,8 @@ Examples
#> Warning: `add_rownames()` was deprecated in dplyr 1.0.0.
#> ℹ Please use `tibble::rownames_to_column()` instead.
#> ℹ The deprecated feature was likely used in the smartid package.
-#> Please report the issue to the authors.
+#> Please report the issue at
+#> <https://github.com/DavisLaboratory/smartid/issues>.
diff --git a/reference/smartid_Package.html b/reference/smartid_Package.html
index fc895a6..08259db 100644
--- a/reference/smartid_Package.html
+++ b/reference/smartid_Package.html
@@ -42,7 +42,13 @@
Changelog
-
+
@@ -52,7 +58,7 @@
Scoring and Marker Selection method based on modified TF-IDF
-
+ Source: R/smartid-package.R
smartid_Package.Rd
diff --git a/reference/tf.html b/reference/tf.html
index 071c0b9..65842e5 100644
--- a/reference/tf.html
+++ b/reference/tf.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
diff --git a/reference/top_markers.html b/reference/top_markers.html
index e6a0295..c992dd3 100644
--- a/reference/top_markers.html
+++ b/reference/top_markers.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
scale score and return top markers
-
+ Source: R/AllGenerics.R, R/top_markers-methods.R
top_markers.Rd
diff --git a/reference/top_markers_abs.html b/reference/top_markers_abs.html
index 57d2ef1..625a3ef 100644
--- a/reference/top_markers_abs.html
+++ b/reference/top_markers_abs.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
calculate group median, MAD or mean score and order genes based on scores
-
+ Source: R/top_markers.R
top_markers_abs.Rd
diff --git a/reference/top_markers_glm.html b/reference/top_markers_glm.html
index 83d3700..f0f1854 100644
--- a/reference/top_markers_glm.html
+++ b/reference/top_markers_glm.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
calculate group mean score using glm and order genes based on scores difference
-
+ Source: R/top_markers.R
top_markers_glm.Rd
diff --git a/reference/top_markers_init.html b/reference/top_markers_init.html
index 64197e4..1a85152 100644
--- a/reference/top_markers_init.html
+++ b/reference/top_markers_init.html
@@ -38,7 +38,13 @@
Changelog
-
+
@@ -48,7 +54,7 @@
compute group summarized score and order genes based on processed scores
-
+ Source: R/top_markers.R
top_markers_init.Rd