analysis/scripts/run_spase_cere4_visium_overall_spatial.R

In lulizou/spASE: Detecting Allele-Specific Expression in Spatial Transcriptomics

library(spacexr)
library(spASE)

res <- readRDS('results/rctd_cere_4_visium.rds')
maternal_counts_matrix <- res@originalSpatialRNA@maternalCounts
paternal_counts_matrix <- res@originalSpatialRNA@paternalCounts
coords <- res@originalSpatialRNA@coords
coords$bead <- rownames(coords)
coords <- coords[c('bead','x','y')]

myfit <- spase(maternal_counts_matrix, paternal_counts_matrix, coords,cores=8)
saveRDS(myfit, file = 'results/results_overall_spatial_cere_4_visium.rds')