| ... | ... |
@@ -98,7 +98,7 @@ setGeneric('runGLOBALBV',
|
| 98 | 98 |
reduction.used = NULL, |
| 99 | 99 |
group.by = NULL, |
| 100 | 100 |
permutation = 100, |
| 101 |
- alternative = c('greater', 'two.sided', 'less'),
|
|
| 101 |
+ alternative = c('two.sided', 'greater', 'less'),
|
|
| 102 | 102 |
add.pvalue = FALSE, |
| 103 | 103 |
random.seed = 1024, |
| 104 | 104 |
action = c("get", "only"),
|
| ... | ... |
@@ -127,7 +127,7 @@ setMethod("runGLOBALBV", "SingleCellExperiment", function(
|
| 127 | 127 |
reduction.used = NULL, |
| 128 | 128 |
group.by = NULL, |
| 129 | 129 |
permutation = 100, |
| 130 |
- alternative = c('greater', 'two.sided', 'less'),
|
|
| 130 |
+ alternative = c('two.sided', "greater", 'less'),
|
|
| 131 | 131 |
add.pvalue = FALSE, |
| 132 | 132 |
random.seed = 1024, |
| 133 | 133 |
action = c("get", "only"),
|
| ... | ... |
@@ -204,10 +204,10 @@ setMethod("runGLOBALBV", "SVPExperiment", function(
|
| 204 | 204 |
reduction.used = NULL, |
| 205 | 205 |
group.by = NULL, |
| 206 | 206 |
permutation = 100, |
| 207 |
- alternative = c('greater', 'two.sided', 'less'),
|
|
| 207 |
+ alternative = c('two.sided', 'greater', 'less'),
|
|
| 208 | 208 |
add.pvalue = FALSE, |
| 209 | 209 |
random.seed = 1024, |
| 210 |
- action = "only", |
|
| 210 |
+ action = c("get", "only"),
|
|
| 211 | 211 |
verbose = TRUE, |
| 212 | 212 |
gsvaexp = NULL, |
| 213 | 213 |
gsvaexp.assay.type = NULL, |
| ... | ... |
@@ -20,7 +20,7 @@ runGLOBALBV( |
| 20 | 20 |
reduction.used = NULL, |
| 21 | 21 |
group.by = NULL, |
| 22 | 22 |
permutation = 100, |
| 23 |
- alternative = c("greater", "two.sided", "less"),
|
|
| 23 |
+ alternative = c("two.sided", "greater", "less"),
|
|
| 24 | 24 |
add.pvalue = FALSE, |
| 25 | 25 |
random.seed = 1024, |
| 26 | 26 |
action = c("get", "only"),
|
| ... | ... |
@@ -44,7 +44,7 @@ runGLOBALBV( |
| 44 | 44 |
reduction.used = NULL, |
| 45 | 45 |
group.by = NULL, |
| 46 | 46 |
permutation = 100, |
| 47 |
- alternative = c("greater", "two.sided", "less"),
|
|
| 47 |
+ alternative = c("two.sided", "greater", "less"),
|
|
| 48 | 48 |
add.pvalue = FALSE, |
| 49 | 49 |
random.seed = 1024, |
| 50 | 50 |
action = c("get", "only"),
|
| ... | ... |
@@ -68,10 +68,10 @@ runGLOBALBV( |
| 68 | 68 |
reduction.used = NULL, |
| 69 | 69 |
group.by = NULL, |
| 70 | 70 |
permutation = 100, |
| 71 |
- alternative = c("greater", "two.sided", "less"),
|
|
| 71 |
+ alternative = c("two.sided", "greater", "less"),
|
|
| 72 | 72 |
add.pvalue = FALSE, |
| 73 | 73 |
random.seed = 1024, |
| 74 |
- action = "only", |
|
| 74 |
+ action = c("get", "only"),
|
|
| 75 | 75 |
verbose = TRUE, |
| 76 | 76 |
gsvaexp = NULL, |
| 77 | 77 |
gsvaexp.assay.type = NULL, |
