Man pages for steverozen/ICAMSxtra
ICAMSxtra
| AnnotateIDVCFsWithTransRanges | Add sequence context and transcript information to an... |
| as.catalog.for.ID115 | Create a catalog from a 'matrix', 'data.frame', or 'vector' |
| Canonicalize1Del115 | Given a deletion and its sequence context, categorize it |
| Canonicalize1ID115 | Given a single insertion or deletion in context categorize... |
| Canonicalize1INS115 | Given an insertion and its sequence context, categorize it. |
| CanonicalizeID115 | Determine the mutation types of insertions and deletions. |
| CatalogRowOrder | Standard order of row names in a catalog |
| Collapse115CatalogTo83 | "Collapse" a catalog |
| CollapseID115CatalogsToID83s | "Collapse" a matrix of ID 115 catalogs to ID 83 catalog |
| CreateOneColID115Matrix | Create one column of the matrix for an indel catalog from... |
| GRCh37.proportions | Genic/intergenic size and proportions for H.sapiens BSgenome... |
| GRCh38.proportions | Genic/intergenic size and proportions for H.sapiens BSgenome... |
| Match1Sig | Find signatures in 'other.sigs' with the highest cosine... |
| MatchSigs1Direction | Find the closest match in 'other.sigs' for each signature in... |
| MatchSigs2Directions | Bidirectional closest similarities between two sets of... |
| MatchSigsAndRelabel | An asymmetrical analysis of a set of "ground truth" and... |
| match_two_sig_sets | Find an optimal matching between two sets of signatures... |
| MeanOfSpectraAsSig | Return the mean of multiple spectra as a signature |
| NumFromId | Get the numerical parts of identifiers. |
| PlotExposure | Plot exposures in multiple plots each with a manageable... |
| PlotExposureInternal | Plot a single exposure plot |
| PlotExposureToPdf | Plot exposures in multiple plots each with a manageable... |
| PlotID115AsID83ToPdf | Plot an ID 115 signatures (default) or catalog as standard... |
| PlotID115Catalog | Plot *one* spectrum or signature |
| PlotID115CatalogToPdf | Plot catalog to a PDF file |
| PlotSpectraAsSigsWithUncertainty | Convert spectra to signatures and then plot mean with "error"... |
| PlotTransBiasID115 | Plot transcription strand bias |
| PlotTransBiasID115ToPdf | Plot transcription strand bias to a PDF file |
| PlotTranscriptionAssociatedDamageToPdf | Plot indel counts on transcribed and nontranscribed strands... |
| ReadExposure | Read an exposure matrix from a file |
| ReadID115Catalog | Read catalog |
| Reverse | Transcription bias of indels classified into 115 categories... |
| Reverse_pooled | Transcription bias of indels classified into 13 categories... |
| sig_dist_matrix | Compute a matrix of distances / similarities between two sets... |
| SortExposure | Sort columns of an exposure matrix from largest to smallest... |
| Target | Transcription bias of indels classified into 115 categories... |
| Target_pooled | Transcription bias of indels classified into 13 categories... |
| TP_FP_FN_avg_sim | Return the numbers of true positives (TP), false positives... |
| VCFsToID115Catalogs | Create ID (small insertion and deletion) catalog from ID VCFs |
| VCFsToID115CatalogsAndPlotToPdf | Read a list of vcfs and plot ID115 catalogs as pdf |
| WriteExposure | Write an exposure matrix to a file |
| WriteID115Catalog | Write a catalog to a file. |
