MakeDF4Regress Define a function to make two dataframe for regression analysis This function was developed based on HSC_multiome_Het_2.ipynb — MakeDF4Regress • redeemR

MakeDF4Regress Define a function to make two dataframe for regression analysis This function was developed based on HSC_multiome_Het_2.ipynb

MakeDF4Regress(
  multiome_wrapper = Donor04_HSC_Multiome_wrapper,
  redeemR = DN4_stemcell_redeemR.seed.sensitive,
  progeny_np = DN4_HSC_LSI_progeny_np,
  assay = "SCT",
  useNPimputation = T,
  maxcloneUMI = 10
)

Arguments

multiome_wrapper: This outject should includes all and more than HSCs cells in redeemR
redeemR: scredeemR object for HSC
progeny_np: run via ProgenyMapping_np
assay: SCT for expression, ATAC for ATAC
useNPimputation: default is T, use all cells called by network propagation, inaddition to the top cells in redeemR
maxcloneUMI: default is 10, Only include genes, in the max clone the expression greater than 10

Value

list(mtx.clone=mtx.clone,mtx.clone.norm.scale=mtx.clone.norm.scale)