Man pages for SingerLab/gac
Genetic Analysis of Cells
| addBinInfo | Adds new columns to the chromInfo |
| addCells | Add cells to an existing cnr |
| addGeneInfo | Adds Gene Information to the gene.index |
| addInfo | Adds new columns to the chromInfo and gene.index |
| add_in_silico_root | build an in-silico root cell and clone profile |
| addPheno | Adds additional phenotypes for a new trait |
| addQC | addQC |
| avg_num_alleles_per_locus | Estimate the estimated number of alleles (copies) per locus |
| binary.cnr | build binary CNR from integer copy number data |
| binaryDDRC | binaryDDRC |
| binary.X | build binary matrix from integer copy number data |
| buildCNR | Build a CNR bundle (Copy Number, -Rounded) |
| cbioportal_copy_number_states | Copy number call categories from ratio data |
| chr_breaks | Estimate chromosome end locations along a continuous genome |
| chr_colors | Generate chromosome sidebar colors |
| chromInfo | Chromosome coordinates and additional data of the bins |
| cluster_heterogeneity | cluster heterogeneity across the sample |
| cnr | cnr: copy number, rounded |
| cnr_data_type | data type in CNR |
| copynumbers | Copy number quantal matrix (copynumbers) |
| create_chromosome_annotation | Create chromosome annotations for custom heatmaps |
| create_chromosome_annotation_bottom | Create chromosome annotations for custom heatmaps |
| create_chromosome_annotation_left | Create chromosome annotations for custom heatmaps |
| create_chromosome_annotation_right | Create chromosome annotations for custom heatmaps |
| create_chromosome_annotation_top | Create chromosome annotations for custom heatmaps |
| dna | dna: a cnr with bulk DNA like copy number data |
| doKSpectral | Run Specral K to select optimum and maximum K from Consensus... |
| estimate_joint_effects | Wrapper to joint CNA effect estimation using GLMNet |
| excludeCells | exclude cells from CNR bundle |
| expand2genes | Expands the bins to genes |
| export_cnr | export CNR to flat text files |
| export_pval_igv | Export the p-values for comparisons of interest to visualize... |
| gac | gac |
| genotype_vdj | Genotype cells at the VDJ recombination sites |
| get_alteration_frequencies | estimate bin and gene alteration frequencies |
| get_cluster_profiles | Build a consensus copy number profile for each cluster or... |
| grch37.genes.5k | Bin-to-gene index |
| HeatmapCNR | HeatmapCNR |
| hg19_cytoBand | HG19 cytoband file from UCSC genome browser |
| histo_logit | Perform logistic regression for a binary/binarized trait |
| histo_logit_cov | perform logistic regression for a binary/binarized trait with... |
| keepCells | keep cells from CNR bundle |
| list_genes_in_region | finds genes within one chromosome interval |
| list_gene_symbols | list out genes |
| lookupCN | Lookup copy number data from bins |
| mapd | Median absolute pairwise deviance (MAPD) |
| mark.genes | Mark genes |
| maximum.percentage | Max percent |
| mid_chr | Estimate chromosome midpoint locations along a continuous... |
| minimum.intersect | Minimum tree.height at the intersect of one-cell and... |
| nbins | number of bins |
| ncells | number of cells in cnr |
| ngenes | number of genes in gene.index |
| npheno | number of phenotypes |
| optClust | Optimizing clustering for single-cell copy number |
| order_bins | order genome bins based on chromosome and starting position |
| order_genes | order gene.index based on chromosome and starting coordinate |
| parctan | Peter Andrew's arctan transformation for visualizing copy... |
| pheno | Single-cell phenotype annotation |
| phylo_cnr | Calculating cell-to-cell distances, heirarchical clustering,... |
| phylo_ddrc | Calculating clone-to-clone distances, and estimating a... |
| plot_ccp | plot consensus clustering |
| plotCL | plot cluster optimization |
| plot_cn_correlations | plot genome wide correlations |
| plot_effect | Genome-wide effects plot |
| plot_frequencies | plot genome-wide amplification and deletion frequencies |
| plot_lr | Manhattan plot of logistic regression output |
| plot_sK | plot kCC vs sK plot kParameter, and stable K from kStats |
| proportion_of_polymorphic_loci | proportion of polymorphic alleles as subclonal |
| pull_gene_copy_numbers | pull a set of copy numbers from a cnr into a data.frame |
| pull_gene_details | Pull gene details for a set of genes |
| qc | Quality control annotation |
| rank_clones | rank clones |
| rle_ddrc | run length encoding to create segment files from DDRC.df |
| roundCNR | rounded quantal matrix |
| run_consensus_clustering | run consensus clustering |
| seg2bins | convert .seg files to match a chromInfo matrix |
| setBrayClusters | Set Bray clusters |
| setKcc | Set cluster membership for K clusters |
| split_cnr | split a cnr by one variable |
| subsetCNR | Subset a set of bins or genes from a CNR object |
| summary_cnr | summary of cnr bundle |
| sync_cnr | sync cnr cells to those in the phenotype annotation |
| vdjBrayClust | VDJ cells clustering based on Bray-Curtis Dissimilarity |
| vdjHeatmap | Heatmap of cells with VDJ recombination |
| vdjPlotClust | plot VDJ clustering |
