fix vignette

Author: samuel-marsh

vignettes/articles/Object_Conversion.Rmd

@@ -68,47 +68,6 @@ pbmc$sample_id <- sample(c("sample1", "sample2", "sample3", "sample4", "sample5"
 ```
 
 
-## Convert Seurat Objects to LIGER Objects
-scCustomize contains the conversion function `as.LIGER()`.  This function has a few advantages over the conversion function `rliger::seuratToLiger()`.  
-
-- `as.liger` will *keep all meta data* and transfer it to LIGER by default.  
-- If a dimensionality reduction is transferred `as.liger` will also store a reduction key for use with scCustomize LIGER plotting functions to correctly set plot axes.  
-- If converting a list of Seurat objects and keeping Seurat variable genes then `as.liger` can either take union or intersection of genes between objects.  
-- `as.liger` has additional internal checks to ensure compatibility with both Seurat V3/4 & V5 object structures.
-
-```{r message=TRUE}
-pbmc_liger <- as.LIGER(x = pbmc, group.by = "sample_id")
-
-pbmc_liger
-```
-
-Confirm that information from meta.data slot was transferred to LIGER object.
-```{r}
-head(colnames(x = [email protected]), 10)
-```
-
-
-
-## Convert LIGER objects to Seurat Objects  
-The liger/rliger package already contains a function `rliger::seuratToLiger()` to convert LIGER objects to Seurat Objects.  However, during this transfer a few things have issues crop up:  
-  
-* All meta data except the "dataset" column from liger_object\@cell.data is lost.
-* Seurat dimensionality reduction is set to tSNE regardless of method used in LIGER analysis
-* Seurat assay name not specified
-
-As of scCustomize v2.1.0 converting to Seurat objects from Liger can be accomplished using `as.liger` function which functions identically to previous function `Liger_to_Seurat()`.  `Liger_to_Seurat()` will continue to work until v2.2.0 at which point it will be completely deprecated.
-
-scCustomize contains modified version of this function which extends the Seurat function [`as.Seurat()`](https://github.com/samuel-marsh/scCustomize/blob/develop/docs/reference/as.Seurat.html) that solves these issues with some extra parameters:   
-  
-* `keep_meta` logical. Whether to keep meta data from the \@cell.data slot in LIGER object.  Default is TRUE.
-* `reduction_label` Name of dimensionality reduction technique used (e.g., tSNE, UMAP, etc).  Ensures dim names are set correctly in Seurat object.
-* `seurat_assay` Name of assay to use for data in Seurat object.  Default is "RNA".  
-* `assay_type` Specify whether to create V3/4 vs V5 Seurat assays.  
-
-```{r message=TRUE}
-new_seurat <- as.Seurat(x = pbmc_liger, reduction_label = "UMAP")
-```
-
 
 ## Convert Seurat or LIGER objects to Anndata objects  
 scCustomize also allows for the conversion of Seurat or LIGER objects to python [anndata](https://anndata.readthedocs.io/en/latest/) objects for analysis in [scanpy](https://scanpy.readthedocs.io/en/stable/) or other compatible python packages via the function `as.anndata`.  These functions were inspired/modified/updated from [sceasy R package](https://github.com/cellgeni/sceasy) (see `as.anndata` documentation).