1. glmGamPoi
  2. NAMESPACE
Browse code

Change 'pseudobulk_sce' to 'pseudobulk'

* Fix bug related to missing assay names
* Support 'n()' inside summary arguments
* Support summarizing a plain matrix

const-ae authored on 03/01/2023 15:39:30
Showing 1 changed files
NAMESPACE
History View file @ 62cbe0a
... ... 
@@ -12,7 +12,7 @@ export(glm_gp)
12 12 
 export(loc_median_fit)
13 13 
 export(overdispersion_mle)
14 14 
 export(overdispersion_shrinkage)
15 
-export(pseudobulk_sce)
15 
+export(pseudobulk)
16 16 
 export(test_de)
17 17 
 export(vars)
18 18 
 import(Rcpp)
Browse code

Change interface of pseudobulk_sce to use 'rlang' idioms

const-ae authored on 24/10/2022 13:58:53
Showing 1 changed files
NAMESPACE
History View file @ 58c0114
... ... 
@@ -14,6 +14,7 @@ export(overdispersion_mle)
14 14 
 export(overdispersion_shrinkage)
15 15 
 export(pseudobulk_sce)
16 16 
 export(test_de)
17 
+export(vars)
17 18 
 import(Rcpp)
18 19 
 import(stats)
19 20 
 importFrom(BiocGenerics,end)
Browse code

Implement 'pseudobulk_sce' to easily form pseudo-bulk samples

const-ae authored on 30/09/2022 13:05:51
Showing 1 changed files
NAMESPACE
History View file @ 7839224
... ... 
@@ -12,6 +12,7 @@ export(glm_gp)
12 12 
 export(loc_median_fit)
13 13 
 export(overdispersion_mle)
14 14 
 export(overdispersion_shrinkage)
15 
+export(pseudobulk_sce)
15 16 
 export(test_de)
16 17 
 import(Rcpp)
17 18 
 import(stats)
Browse code

Fix problems in documentation

const-ae authored on 08/01/2021 15:35:52
Showing 1 changed files
NAMESPACE
History View file @ 1e4ae26
... ... 
@@ -15,6 +15,8 @@ export(overdispersion_shrinkage)
15 15 
 export(test_de)
16 16 
 import(Rcpp)
17 17 
 import(stats)
18 
+importFrom(BiocGenerics,end)
19 
+importFrom(BiocGenerics,width)
18 20 
 importFrom(SummarizedExperiment,assay)
19 21 
 importFrom(methods,as)
20 22 
 importFrom(methods,canCoerce)
Browse code

Start implementation of predict()

const-ae authored on 05/01/2021 13:11:00
Showing 1 changed files
NAMESPACE
History View file @ 726fa97
... ... 
@@ -3,6 +3,7 @@
3 3 
 S3method(as.list,glmGamPoi)
4 4 
 S3method(format,glmGamPoi)
5 5 
 S3method(format,summary.glmGamPoi)
6 
+S3method(predict,glmGamPoi)
6 7 
 S3method(print,glmGamPoi)
7 8 
 S3method(print,summary.glmGamPoi)
8 9 
 S3method(residuals,glmGamPoi)
Browse code

Export loc_median_fit and extend its documentation

const-ae authored on 24/08/2020 10:36:45
Showing 1 changed files
NAMESPACE
History View file @ 8067e76
... ... 
@@ -8,6 +8,7 @@ S3method(print,summary.glmGamPoi)
8 8 
 S3method(residuals,glmGamPoi)
9 9 
 S3method(summary,glmGamPoi)
10 10 
 export(glm_gp)
11 
+export(loc_median_fit)
11 12 
 export(overdispersion_mle)
12 13 
 export(overdispersion_shrinkage)
13 14 
 export(test_de)
Browse code

Include data in object returned by glm_gp

* Change the method signature of residuals.glmGamPoi and test_de()

const-ae authored on 08/06/2020 10:31:12
Showing 1 changed files
NAMESPACE
History View file @ 7d3171f
... ... 
@@ -13,6 +13,7 @@ export(overdispersion_shrinkage)
13 13 
 export(test_de)
14 14 
 import(Rcpp)
15 15 
 import(stats)
16 
+importFrom(SummarizedExperiment,assay)
16 17 
 importFrom(methods,as)
17 18 
 importFrom(methods,canCoerce)
18 19 
 importFrom(methods,is)
Browse code

Rename shrink_ql_dispersion() -> overdispersion_shrinkage()

* Export function
* Document behavior
* Clean up the arguments for overdispersion_shrinkage() and
variance_prior()

const-ae authored on 05/06/2020 14:57:38
Showing 1 changed files
NAMESPACE
History View file @ 88dd545
... ... 
@@ -9,6 +9,7 @@ S3method(residuals,glmGamPoi)
9 9 
 S3method(summary,glmGamPoi)
10 10 
 export(glm_gp)
11 11 
 export(overdispersion_mle)
12 
+export(overdispersion_shrinkage)
12 13 
 export(test_de)
13 14 
 import(Rcpp)
14 15 
 import(stats)
Browse code

Rename gampoi_test_qlr() -> test_de()

const-ae authored on 05/06/2020 12:32:57
Showing 1 changed files
NAMESPACE
History View file @ fe2435a
... ... 
@@ -7,9 +7,9 @@ S3method(print,glmGamPoi)
7 7 
 S3method(print,summary.glmGamPoi)
8 8 
 S3method(residuals,glmGamPoi)
9 9 
 S3method(summary,glmGamPoi)
10 
-export(gampoi_test_qlr)
11 10 
 export(glm_gp)
12 11 
 export(overdispersion_mle)
12 
+export(test_de)
13 13 
 import(Rcpp)
14 14 
 import(stats)
15 15 
 importFrom(methods,as)
Browse code

Rename gampoi_overdispersion_mle -> overdispersion_mle

const-ae authored on 05/06/2020 12:05:26
Showing 1 changed files
NAMESPACE
History View file @ 0a99216
... ... 
@@ -7,9 +7,9 @@ S3method(print,glmGamPoi)
7 7 
 S3method(print,summary.glmGamPoi)
8 8 
 S3method(residuals,glmGamPoi)
9 9 
 S3method(summary,glmGamPoi)
10 
-export(gampoi_overdispersion_mle)
11 10 
 export(gampoi_test_qlr)
12 11 
 export(glm_gp)
12 
+export(overdispersion_mle)
13 13 
 import(Rcpp)
14 14 
 import(stats)
15 15 
 importFrom(methods,as)
Browse code

Add quasi-likelihood ratio test

const-ae authored on 28/05/2020 06:57:12
Showing 1 changed files
NAMESPACE
History View file @ 046e8c2
... ... 
@@ -8,6 +8,7 @@ S3method(print,summary.glmGamPoi)
8 8 
 S3method(residuals,glmGamPoi)
9 9 
 S3method(summary,glmGamPoi)
10 10 
 export(gampoi_overdispersion_mle)
11 
+export(gampoi_test_qlr)
11 12 
 export(glm_gp)
12 13 
 import(Rcpp)
13 14 
 import(stats)
Browse code

Add as.list.glmGamPoi() function

const-ae authored on 14/04/2020 12:09:48
Showing 1 changed files
NAMESPACE
History View file @ 83dc724
... ... 
@@ -1,5 +1,6 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+S3method(as.list,glmGamPoi)
3 4 
 S3method(format,glmGamPoi)
4 5 
 S3method(format,summary.glmGamPoi)
5 6 
 S3method(print,glmGamPoi)
Browse code

Implement residual function

const-ae authored on 27/02/2020 15:25:58
Showing 1 changed files
NAMESPACE
History View file @ fa82e05
... ... 
@@ -4,6 +4,7 @@ S3method(format,glmGamPoi)
4 4 
 S3method(format,summary.glmGamPoi)
5 5 
 S3method(print,glmGamPoi)
6 6 
 S3method(print,summary.glmGamPoi)
7 
+S3method(residuals,glmGamPoi)
7 8 
 S3method(summary,glmGamPoi)
8 9 
 export(gampoi_overdispersion_mle)
9 10 
 export(glm_gp)
Browse code

Export printing stuff so it works also elsewhere

const-ae authored on 31/01/2020 13:51:25
Showing 1 changed files
NAMESPACE
History View file @ e236ca1
... ... 
@@ -1,5 +1,10 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+S3method(format,glmGamPoi)
4 
+S3method(format,summary.glmGamPoi)
5 
+S3method(print,glmGamPoi)
6 
+S3method(print,summary.glmGamPoi)
7 
+S3method(summary,glmGamPoi)
3 8 
 export(gampoi_overdispersion_mle)
4 9 
 export(glm_gp)
5 10 
 import(Rcpp)
Browse code

Improve documentation

const-ae authored on 28/01/2020 12:02:48
Showing 1 changed files
NAMESPACE
History View file @ 25481db
... ... 
@@ -2,7 +2,6 @@
2 2
3 3 
 export(gampoi_overdispersion_mle)
4 4 
 export(glm_gp)
5 
-export(glm_gp_impl)
6 5 
 import(Rcpp)
7 6 
 import(stats)
8 7 
 importFrom(methods,as)
Browse code

Fix spelling and imports

const-ae authored on 28/01/2020 10:17:23
Showing 1 changed files
NAMESPACE
History View file @ fd7732a
... ... 
@@ -5,5 +5,8 @@ export(glm_gp)
5 5 
 export(glm_gp_impl)
6 6 
 import(Rcpp)
7 7 
 import(stats)
8 
-importFrom(Matrix,t)
8 
+importFrom(methods,as)
9 
+importFrom(methods,canCoerce)
10 
+importFrom(methods,is)
11 
+importFrom(utils,head)
9 12 
 useDynLib(glmGamPoi, .registration = TRUE)
Browse code

Add bare-bones documentation

const-ae authored on 23/01/2020 08:57:51
Showing 1 changed files
NAMESPACE
History View file @ 5090998
... ... 
@@ -5,4 +5,5 @@ export(glm_gp)
5 5 
 export(glm_gp_impl)
6 6 
 import(Rcpp)
7 7 
 import(stats)
8 
+importFrom(Matrix,t)
8 9 
 useDynLib(glmGamPoi, .registration = TRUE)
Browse code

Fix some R CMD check problems

const-ae authored on 20/01/2020 14:01:18
Showing 1 changed files
NAMESPACE
History View file @ 3086dff
... ... 
@@ -3,4 +3,6 @@
3 3 
 export(gampoi_overdispersion_mle)
4 4 
 export(glm_gp)
5 5 
 export(glm_gp_impl)
6 
+import(Rcpp)
7 
+import(stats)
6 8 
 useDynLib(glmGamPoi, .registration = TRUE)
Browse code

Implement bandara_overdispersion_mle

const-ae authored on 16/01/2020 14:27:33
Showing 1 changed files
NAMESPACE
History View file @ 4778c79
... ... 
@@ -1,5 +1,6 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export(gampoi_overdispersion_mle)
3 4 
 export(glm_gp)
4 5 
 export(glm_gp_impl)
5 
-export(gp_overdispersion_mle)
6 
+useDynLib(glmGamPoi, .registration = TRUE)
Browse code

Build skeleton of the most important functions

const-ae authored on 15/01/2020 15:53:25
Showing 1 changed files
NAMESPACE
History View file @ cffee5e
... ... 
@@ -1 +1,5 @@
1 
-exportPattern("^[[:alpha:]]+")
1 
+# Generated by roxygen2: do not edit by hand
2 
+
3 
+export(glm_gp)
4 
+export(glm_gp_impl)
5 
+export(gp_overdispersion_mle)
Browse code

Initial commit

const-ae authored on 15/01/2020 15:16:07
Showing 1 changed files
NAMESPACE
History View file @ 0e86863
1 1 
new file mode 100644
... ... 
@@ -0,0 +1 @@
1 
+exportPattern("^[[:alpha:]]+")