| 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 |
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