# R package for Regulatory multi-omics with Deep Mitochondrial mutation profiling

## Documentation for package ‘redeemR’ version 1.0

- DESCRIPTION file.

## Help Pages

AddDatatoplot_clustering | AddDatatoplot_clustering This prepare the clonal clustering data to plot
AddDatatoplot_clustering-method | AddDatatoplot_clustering This prepare the clonal clustering data to plot
AddDist | AddDist This add Jaccard, Dice, Jaccard3W distance and stored in DistObjects
AddDist-method | AddDist This add Jaccard, Dice, Jaccard3W distance and stored in DistObjects
AddDist_legacy | AddDist_legacy This add Jaccard, Dice, Jaccard3W distance and stored in DistObjects
AddDist_legacy-method | AddDist_legacy This add Jaccard, Dice, Jaccard3W distance and stored in DistObjects
AddHemSignature | Function to add hematopoietic signatures from Griffin_Signatures
AddTree | Add_Tree Optional, if a phylogentic tree object phylo is already available, can be directly added to the redeemR
AddTree-method | Add_Tree Optional, if a phylogentic tree object phylo is already available, can be directly added to the redeemR class in slot TREE
Add_AssignVariant | Add_AssignVariant a function to assign variants to edges based on maximum likihood
Add_AssignVariant-method | a function to assign variants to edges based on maximum likihood
Add_DepthMatrix | Add_DepthMatrix Optional, add a matrix with same dimension with the Cts.Mtx and Cts.Mtx.bi, which display the depths
Add_DepthMatrix-method | Add_DepthMatrix Optional, add a matrix with same dimension with the Cts.Mtx and Cts.Mtx.bi, which display the depths
add_derived_profile_info | This is a convinience function, internal borrowed from https://github.com/NickWilliamsSanger/treemut/blob/main/R/treemut.R#L68
Add_tree_cut | Add_tree_cut a function to cut tree using assigned variant as branch-length on edge
Add_tree_cut-method | a function to cut tree using assigned variant as branch-length on edge
ATAC_Wrapper | Wrap Seurat ATAC clustering
BinaryDist | Compute distances for binary distances
Clone_FinderMarker | Define a function to perform Find marker for top vs bottom clones This function was developed based on DN4T2.basics.ipynb
ComputeRejectRate | Function to compute the reject rate(The filtering rate in concensus variant calling)
convert_mitotracing_redeemR | convert_mitotracing_redeemR
CountVperCell | Internal function in plot_variant
Create_mitoTracing | Create_mitoTracing
Create_redeemR | Create_redeemR
CV | Internal CV
CW_mgatk.read | Old Function to read in redeemV outputs It process the data same way as redeemR.read but simultanously reading in all threadhold as a list This function allows you to read raw data from XX/final folder, the output from redeemV
Datatoplots | An intermediate S4 class Datatoplots
Datatoplots-class | An intermediate S4 class Datatoplots
DE.gettripple | DE.gettripple
DepthSummary | Function to summarize the depth (Total that passed Q30)
df2ProfileMtx | This is a convinience function, internal
DistObjects | An intermediate S4 class Datatoplots
DistObjects-class | An intermediate S4 class Datatoplots
DoDE | DoDE
FromDist2Graph | FromDist2Graph From distance object or matrix to graph, default is to return igraph object This function was developed based on
GEM_Wrapper | Wrap Seurat RNA clustering
get_ancestral_nodes | This is a convinience function, internal borrowed from https://github.com/NickWilliamsSanger/treemut/blob/main/R/treemut.R#L68
Get_Clonal_Variants | Get_Clonal_Variants
GTSummary | Function to generate GTS summary
LineageBiasPlot | plot_npSummary to plot the lineage composition
MakeAllNodes | Define a function make the Allnodes(Node|Parent|Freq|CladeSize), where Freq is the number of variants assigned to the node(as ending point) from redeemR object,
MakeDF4Regress | MakeDF4Regress Define a function to make two dataframe for regression analysis This function was developed based on HSC_multiome_Het_2.ipynb
MakeNN | Define a function to make nn list, which can be further used to make adjacency matrix This scan row by row, looking for k.param nearest neighbours
Make_AnnTable | 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
Make_Cells4Nodes | Define a function to make a list, each contains the cell names for a node
Make_matrix | Make_matrix This will make the matixies of Cell VS mitochondrial variants and return redeemR Results stored in Cts.Mtx and Cts.Mtx.bi
Make_matrix-method | Make_matrix This will make the matixies of Cell VS mitochondrial variants and return redeemR Results stored in Cts.Mtx and Cts.Mtx.bi
Make_tree | Make_tree This will generate a basic phylogenetic tree
Make_tree-method | Make_tree This will generate a basic phylogenetic tree
Make_tree_legacy | Make_tree_legacy This will generate a basic phylogenetic tree
Make_tree_legacy-method | Make_tree_legacy This will generate a basic phylogenetic tree
MergeMtx | Function to Merge sparse Matrix
mitoTracing | Legacy function: Major mitoTracing class that store clonal-resolved multi-omics
mitoTracing-class | Legacy function: Major mitoTracing class that store clonal-resolved multi-omics
Motifenrich.binom | Motifenrich.binom In house function to compute enrichment from Fimo This function was developed based on HSC_multiome_Het.ipynb and HSC_multiome_Het_2.ipynb
Multi_Wrapper | Wrap Seurat Multiomics clustering
MutationProfile.bulk | Function to plot bulk level mutation signatures
NN2M | Define a function convert nn list to adjacency matrix that can be further used for igraph
plot_depth | Function to plot the mito depth summary
plot_depth_legacy | Legacy Function to plot the mito depth summary
plot_npSummary | plot_npSummary to assess the outputlevel
plot_variant | Function to plot variant metrics
plot_variant_legacy | Legacy Function to plot variant metrics
ProgenyMapping | Define a function to perform single-cell based hard porogeny assignment This function was developed based on DN4T2.basics.ipynb
ProgenyMapping_np | ProgenyMapping_np Define a function to compute network propagation based probability FromDist2Graph is needed to convert fistance matrix into MNN graph
quick_w_cosine | Compute weighted cosine distance
quick_w_jaccard | Compute weighted jaccard distance
Reclustering | Function to reclustering a seurat object
Reclustering_hm | Function to reclustering_hm a seurat object with Harmony
reconstruct_genotype_summary | This is a function borrowed from https://github.com/NickWilliamsSanger/treemut/blob/main/R/treemut.R#L68 Input phylo object, return a "profile matrix"-Edge(or denoted as the ending node) vs cell. a 0, 1 character string that indicate what cells in a given node
redeemR | Major redeem class that store clonal-resolved multi-omics
redeemR-class | Major redeem class that store clonal-resolved multi-omics
redeemR.read | Function to read in redeemV outputs
Runplot_scale_2 | plot_npSummary to assess the outputlevel vs lineage bias, normalize by assigned
Runplot_scale_3 | plot_npSummary to assess the outputlevel vs lineage bias, normalize by HSC original clone size
Run_Lin_regression | Run_Lin_regression
Run_Lin_regression_poi | Run_Lin_regression_poi Firstly used in HSC_multiome_Het_2.ipynb This function was developed based on
SeuratLSIClustering | SeuratLSIClustering This will use the mito variants for Seurat clustering (LSI based)
SeuratLSIClustering-method | SeuratLSIClustering This will use the mito variants for Seurat clustering (LSI based)
show-method | show This will show the basics of redeemR class
Show_Consensus | Function to plot consensus mtDNA mutation benchmark
split_profile | This is a convinience function, internal borrowed from https://github.com/NickWilliamsSanger/treemut/blob/main/R/treemut.R#L68
str2vector | This is a convinience function, internal
Subset_redeemR | Subset_redeemR Subset a redeemR object by selecting a subset of cells, return a new redeemR object with only 4 slots: para; CellMeta; Cts.Mtx.bi; UniqueV, can be used for downstreme compute distance, clonal clustering, make tree, etc
Tomerge_v2 | Tomerge_v2
Translate_RNA2ATAC | Function to translate the RNA barcode into ATAC barcode and add a column
Translate_simple_ATAC2RNA | Translate_simple_ATAC2RNA
Translate_simple_RNA2ATAC | Translate_simple_RNA2ATAC
TREE | An intermediate S4 class Tree that store tree info
TREE-class | An intermediate S4 class Tree that store tree info
Vfilter_v3 | Function to filter variants, deprecated
Vfilter_v4 | Function to filter variants, v4