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Make_AnnTable, Make a big dataframe, each row is a cell, each column includes info such as clonal UMAP, Clonal ID, ATAC/RNA/WNN UMAP, PCA, gene expression of chosen gene, etc. Require a redeemR object and a multiome wrapper that better matches the cells in the redeemR

Source: R/buid_tree.R
Make_AnnTable.Rd

Make_AnnTable, Make a big dataframe, each row is a cell, each column includes info such as clonal UMAP, Clonal ID, ATAC/RNA/WNN UMAP, PCA, gene expression of chosen gene, etc. Require a redeemR object and a multiome wrapper that better matches the cells in the redeemR

Usage

Make_AnnTable(
  redeemR = DN4_HSC_redeemR.Sensitive,
  Multiome = Donor04_HSC_Multiome_wrapper,
  clonal_features = c("nCount_mitoV", "seurat_clusters"),
  clonal_features_rename = c("nCount_mitoV", "clone_clusters"),
  CellMeta_features = c("meanCov", "nCount_RNA", "nFeature_RNA", "nCount_ATAC",
    "nFeature_ATAC", "CellType"),
  CellMeta_features_rename = c("Mito_meanCov", "nCount_RNA", "nFeature_RNA",
    "nCount_ATAC", "nFeature_ATAC", "CellType"),
  multiome_features = c("seurat_clusters"),
  multiome_features_rename = c("NewSeurat_cluster"),
  RNAUMAP = T,
  ATACUMAP = T,
  WNNUMAP = T,
  PCA = F,
  LSI = F,
  Variants = "",
  genes = "",
  peaks = "",
  PostTrans_from = c(2, 3),
  PostTrans_to = c(2, 1)
)

Arguments

redeemR

eg. DN4_HSC_redeemR.Sensitive

Multiome

eg. Donor04_HSC_Multiome_wrapper, Multiome_wrapper object that matches with the redeemR, a reclustering using Multi_Wrapper() is recommended

clonal_features

eg. c("nCount_mitoV","seurat_clusters"), The column names take from redeemR@Seurat@meta.data, importantly the clonal clusterings

clonal_features_rename

eg. c("nCount_mitoV","clone_clusters") Rename the clonal_features

CellMeta_features

eg. c("meanCov","nCount_RNA","nFeature_RNA","nCount_ATAC","nFeature_ATAC","CellType") The column names take from redeemR@CellMeta, may useful cell features

CellMeta_features_rename

eg. c("Mito_meanCov","nCount_RNA","nFeature_RNA","nCount_ATAC","nFeature_ATAC","CellType") Rename the CellMeta

multiome_features

eg. c("seurat_clusters") The column names take from Multiome@meta.data

multiome_features_rename

eg. c("NewSeurat_cluster") Rename the column names for multiome_features

RNAUMAP

default T

ATACUMAP

Default T

WNNUMAP

Default T

PCA

Default T

LSI

Default T

Variants

Default "" can be a vector of variant names format is eg "Variants10020TC"

genes

Default "" can be a vector of gene names, for example c("HLF","CD34")

peaks

Default "" can be a vector of peaks names

PostTrans_from

Default c(2,3) # This is a tricky part eh nmerging files are involved, find the postfix from cellranger agg for different sample

PostTrans_to

Default c(2,1)

Value

AnnTable