ProgenyMapping_np Define a function to compute network propagation based probability FromDist2Graph is needed to convert fistance matrix into MNN graph

ProgenyMapping_np Define a function to compute network propagation based probability FromDist2Graph is needed to convert fistance matrix into MNN graph

Usage

ProgenyMapping_np(
  HSC_redeemR = DN4_stemcell_redeemR.seed.verysensitive,
  Full_redeemR = DN4_BMMC_HSPC_HSC_redeemR.verysensitive,
  CloneCol = "Clone_merge",
  k = 30,
  gm = 0.5,
  useLSI = F,
  useSCAVENGE_LSI = F,
  subsample = F,
  ProbCut = 0.7,
  Celltype = "Rig.CellType"
)

Arguments

HSC_redeemR

The HSC_redeemR is the redeemR object for defined HSC, have already gone through Add_DepthMatrix--Add_AssignVariant--Add_tree_cut, otherwise, need othereise, need a column in CellMeta that indicates the clone ID

Full_redeemR

The FULL_redeemR is the redeemR object for the full BMMC_HSPC_HSC

CloneCol

"Clone_merge"

k

the k.param used for MNN graph

gm

gamma default is 0.05 which mean 95% information is passing out

ProbCut

The cutoff of the maximum probability for a given progeny cell(If the maximum probability is lower than ProbCut, it will be filtered)

Celltype

The column to be used in aggregate into lineages

Value

a list of two ALLmeta.npClone (A meta data with last column npClone), np_mat (the network propagation matrix))