Define a function to perform Find marker for top vs bottom clones This function was developed based on DN4T2.basics.ipynb

Define a function to perform Find marker for top vs bottom clones This function was developed based on DN4T2.basics.ipynb

Clone_FinderMarker(
  topClones,
  bottomClones,
  HSC_Multiome_wrapper = Donor04_HSC_Multiome_wrapper,
  HSC_redeemR,
  assay = "SCT",
  test = "wilcox"
)

Arguments

topClones

a vector of clone ID eg. c("1","3","7"),this must be in HSC_redeemR@CellMeta$Clone_merge

bottomClones

a vector of clone ID eg. c("2","5"), this must be in HSC_redeemR@CellMeta$Clone_merge

HSC_redeemR

redeemR object for HSC

test

the statistic method to use for DE, a wrapper function from Seurat FindAllMarkers

ob

Seurat object (Multiomics), the postfix needs to be compatible with HSC_redeemR, the cells will be matched by cell names