MakeDF4Regress: MakeDF4Regress Define a function to make two dataframe for...

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

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

Description

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

Usage

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)

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