Data structures, clustering and testing for single cell immune
receptor repertoires (scRNAseq RepSeq/AIRR-seq)
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Documentation for package ‘CellaRepertorium’ version 1.10.0
Help Pages
| $-method | Access public members of ContigCellDB object. |
| $<--method | Access public members of ContigCellDB object. |
| .cluster_permute_test | Cell permutation tests (internal) |
| canonicalize_cell | Find a canonical contig to represent a cell |
| canonicalize_cluster | Find a canonical contig to represent a cluster |
| ccdb_ex | A preconstructed 'ContigClusterDB' from the 'contigs_qc' data |
| ccdb_join | Join dataframe or SingleCellExperiment object with ContigCellDB object |
| cdhit | R interface to CDHIT/CDHITest |
| cdhit_ccdb | Use 'cdhit()' to cluster a 'ContigCellDB()' |
| cland | Cluster "And" intersection |
| cluster_filterset | A filtration of clusters |
| cluster_germline | Cluster contigs by germline properties |
| cluster_logistic_test | Test clusters for differential usage |
| cluster_permute_test | Tests for independence between labels and covariates using permutation of cells |
| cluster_plot | Make a plot showing properties of the clustering |
| cluster_test_by | Test clusters for differential usage |
| ContigCellDB | Construct a ContigCellDB |
| ContigCellDB-mutate | Access public members of ContigCellDB object. |
| ContigCellDB_10XVDJ | Construct a ContigCellDB |
| contigs_qc | Filtered and annotated contigs of TCR from mice |
| crosstab_by_celltype | Count contig UMIs by celltype |
| cross_tab_tbl | Generate a 2d cross tab using arbitrary numbers of columns as factors |
| dim-method | 'data.frame'-like mutation/accessor generics for 'ContigCellDB' objects |
| dimnames-method | 'data.frame'-like mutation/accessor generics for 'ContigCellDB' objects |
| entropy | Calculate the entropy of a vector |
| enumerate_pairing | Categorize the pairing present in a cell |
| equalize_ccdb | Take the intersection of keys in tables in 'x' |
| fancy_name_contigs | Generate a legible name for a series of contigs |
| filter_cdb | Create new or update existing columns of 'ContigCellDB' tables |
| fine_clustering | Perform additional clustering of sequences within groups |
| fine_cluster_seqs | Calculate distances and perform hierarchical clustering on a set of sequences |
| generate_pseudobulk | Generate "pseudobulk" data from a 'ContigCellDB' |
| guess_celltype | Guess the cell type of a contig from the chain ID |
| hushWarning | Selectively muffle warnings based on output |
| ig_chain_recode | Categorize the pairing present in a cell |
| left_join_warn | Perform a 'dplyr::left_join()' but check for non-key overlapping fields |
| map_axis_labels | Color axis labels |
| modal_category | Calculate the entropy of a vector |
| mutate_cdb | Create new or update existing columns of 'ContigCellDB' tables |
| ncol-method | 'data.frame'-like mutation/accessor generics for 'ContigCellDB' objects |
| np | Calculate the entropy of a vector |
| nrow-method | 'data.frame'-like mutation/accessor generics for 'ContigCellDB' objects |
| pairing_tables | Generate a list of tables representing clusters paired in cells |
| plot_cluster_factors | Visualization of pairs of cluster factor |
| plot_permute_test | Plot a histogram of permuted vs observed test statistic |
| print.PermuteTest | Plot a histogram of permuted vs observed test statistic |
| print.PermuteTestList | Plot a histogram of permuted vs observed test statistic |
| purity | Calculate number of cluster-subject singletons for the purposes of permutation testing |
| rank_chain_ccdb | Rank contigs, per cell, by experiment-wide prevalence of 'cluster_pk', which is added as the 'prevalence' field |
| rank_prevalence_ccdb | Rank contigs, per cell, by experiment-wide prevalence of 'cluster_pk', which is added as the 'prevalence' field |
| rbind-method | Combine 'ContigCellDB' along rows (contigs, cells or clusters). |
| rbind.ContigCellDB | Combine 'ContigCellDB' along rows (contigs, cells or clusters). |
| reexports | Turn an object into a tidy tibble |
| right_join_warn | Perform a 'dplyr::left_join()' but check for non-key overlapping fields |
| split_cdb | Split into a list of 'ContigCellDB()' by named fields |
| tcr_chain_recode | Categorize the pairing present in a cell |
| tidy | Turn an object into a tidy tibble |
| tidy.PermuteTest | Plot a histogram of permuted vs observed test statistic |
| tidy.PermuteTestList | Plot a histogram of permuted vs observed test statistic |
| [-method | 'data.frame'-like mutation/accessor generics for 'ContigCellDB' objects |
| [[-method | 'data.frame'-like mutation/accessor generics for 'ContigCellDB' objects |