| ... | ... |
@@ -53,6 +53,18 @@ if (!requireNamespace("BiocManager", quietly = TRUE)) {
|
| 53 | 53 |
BiocManager::install("sales-lab/spatialDE")
|
| 54 | 54 |
``` |
| 55 | 55 |
|
| 56 |
+ |
|
| 57 |
+## Basic usage |
|
| 58 |
+ |
|
| 59 |
+```{r usage, eval=TRUE}
|
|
| 60 |
+library(spatialDE) |
|
| 61 |
+spe <- mockSVG(return_SPE = TRUE) |
|
| 62 |
+de_results <- spatialDE(spe) |
|
| 63 |
+head(de_results) |
|
| 64 |
+``` |
|
| 65 |
+ |
|
| 66 |
+ |
|
| 67 |
+ |
|
| 56 | 68 |
## Citation |
| 57 | 69 |
|
| 58 | 70 |
<!-- TODO: update once pkg on BioC --> |
| ... | ... |
@@ -45,6 +45,36 @@ if (!requireNamespace("BiocManager", quietly = TRUE)) {
|
| 45 | 45 |
BiocManager::install("sales-lab/spatialDE")
|
| 46 | 46 |
``` |
| 47 | 47 |
|
| 48 |
+## Basic usage |
|
| 49 |
+ |
|
| 50 |
+``` r |
|
| 51 |
+library(spatialDE) |
|
| 52 |
+spe <- mockSVG(return_SPE = TRUE) |
|
| 53 |
+de_results <- spatialDE(spe) |
|
| 54 |
+head(de_results) |
|
| 55 |
+#> FSV M g l max_delta max_ll max_mu_hat max_s2_t_hat |
|
| 56 |
+#> 0 6.893971e-01 4 Gene_0001 0.5 4.480494e-01 -12.5057349 -44.97443 1.016237e+03 |
|
| 57 |
+#> 1 2.049747e-09 4 Gene_0002 0.5 4.851652e+08 -23.3349972 -25.89877 1.382703e-06 |
|
| 58 |
+#> 2 2.049747e-09 4 Gene_0003 0.5 4.851652e+08 -3.8319606 -47.30915 4.613312e-06 |
|
| 59 |
+#> 3 2.049747e-09 4 Gene_0004 0.5 4.851652e+08 -0.8721812 -51.75744 5.521607e-06 |
|
| 60 |
+#> 4 2.049747e-09 4 Gene_0006 0.5 4.851652e+08 -22.7027842 -22.22222 1.018043e-06 |
|
| 61 |
+#> 5 2.049747e-09 4 Gene_0008 0.5 4.851652e+08 -1.4240589 -43.55167 3.909613e-06 |
|
| 62 |
+#> model n s2_FSV s2_logdelta time BIC max_ll_null |
|
| 63 |
+#> 0 SE 100 4.1604136 9.981394e+01 0.001912832 43.43215 -13.070591 |
|
| 64 |
+#> 1 SE 100 0.6775166 1.167603e+17 0.003101826 65.09068 -23.337514 |
|
| 65 |
+#> 2 SE 100 0.1014734 1.748749e+16 0.003578186 26.08460 -3.834477 |
|
| 66 |
+#> 3 SE 100 2.1406586 3.689118e+17 0.003778219 20.16504 -0.874698 |
|
| 67 |
+#> 4 SE 100 11.2472218 1.938297e+18 0.002474070 63.82625 -22.705301 |
|
| 68 |
+#> 5 SE 100 0.4912790 8.466489e+16 0.004010916 21.26880 -1.426576 |
|
| 69 |
+#> LLR pval qval |
|
| 70 |
+#> 0 0.564856105 0.4523102 0.9599889 |
|
| 71 |
+#> 1 0.002516790 0.9599888 0.9599889 |
|
| 72 |
+#> 2 0.002516786 0.9599888 0.9599889 |
|
| 73 |
+#> 3 0.002516791 0.9599888 0.9599889 |
|
| 74 |
+#> 4 0.002516792 0.9599888 0.9599889 |
|
| 75 |
+#> 5 0.002516790 0.9599888 0.9599889 |
|
| 76 |
+``` |
|
| 77 |
+ |
|
| 48 | 78 |
## Citation |
| 49 | 79 |
|
| 50 | 80 |
<!-- TODO: update once pkg on BioC --> |
