Commit 260e2207 authored by Anne  BITON's avatar Anne BITON
Browse files

correct paths and assay ID

parent 7b9f963a
......@@ -39,7 +39,7 @@ library(EGSEA)
dirdata <- "../../data/"
#dirdata <- '/Volumes/scEMPs/scmce/data/'
dirtrajectories <- paste0(dirdata,'derived/YS_library123/trajectories/')
dirtrajectories <- paste0(dirdata,'derived/YS/trajectories/')
dir.create(dirtrajectories)
```
......@@ -48,21 +48,21 @@ dir.create(dirtrajectories)
```{r}
filesce <- paste0(dirdata, "derived/YS_library123/YS_sceall_seurat_fastMNN_bycondbyrun_withoutMitoGenes.rda")
filesce <- paste0(dirdata, "derived/YS/YS_sceall_seurat_fastMNN_bycondbyrun_withoutMitoGenes.rda")
base::load(filesce)
```
```{r}
mart <- useMart(biomart="ensembl", dataset="mmusculus_gene_ensembl")
geneAnnot <- biomaRt::getBM(values = rownames(sceall_seurat@assays$RNA_raw@data),
geneAnnot <- biomaRt::getBM(values = rownames(sceall_seurat@assays$RNA@data),
attributes = c('mgi_symbol', 'mgi_id', 'entrezgene_id','description', 'chromosome_name','start_position', 'end_position', 'strand', 'gene_biotype'),
filters = 'mgi_symbol', mart=mart)
geneAnnot$mgi_id <- paste0('http://www.informatics.jax.org/marker/',geneAnnot$mgi_id)
# add ensembl with missing annotations
geneAnnot <- rbind(geneAnnot,
data.frame(mgi_symbol = setdiff(rownames(sceall_seurat@assays$RNA_raw@data), geneAnnot$mgi_symbol),
data.frame(mgi_symbol = setdiff(rownames(sceall_seurat@assays$RNA@data), geneAnnot$mgi_symbol),
mgi_id=NA, entrezgene_id=NA, description=NA, chromosome_name=NA,
start_position=NA, end_position=NA, strand=NA, gene_biotype=NA))
......
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