ProgenyMapping_np: ProgenyMapping_np Define a function to compute network...

In chenweng1991/scMitoTracing: R package for Regulatory multi-omics with Deep Mitochondrial mutation profiling

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

Description

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))

chenweng1991/scMitoTracing documentation built on July 2, 2024, 8:41 p.m.