Man pages for arcolombo/TxDbLite
Lightweight SQLite-based annotation classes/packages for use with arkas
| ArrayControlDbLite | Constructor for an ArrayControlDbLite object. |
| chrs | helper function for findDupes |
| createAnnotationPackage | create an annotation package for a FASTA file (try to figure... |
| EnsDbLite | Constructor for an EnsDbLite object. |
| ensDbLiteFromFasta | Function to create an EnsDbLite object (a stripped-down... |
| ensembl_biotypes | Structure for annotating transcript biotypes from ENSEMBL |
| ensemblToReactome | Data frame of ENSEMBL transcript IDs and corresponding... |
| ERCC_annotated | Data frame of External RNA-Control-Consortium (ERCC) Ambion... |
| ErccDbLite | Constructor for an ErccDbLite object. |
| erccDbLiteFromFasta | create an ERCC annotation DB from the FASTA file NOTE: we... |
| fetchFromEnsembl | a wrapper for biomaRt::getBM |
| findDupes | find any duplicate seqnames in FASTA files BEFORE creating an... |
| getAnnotationType | (try to) figure out what type of annotation package to create |
| getDupeSeq | helper function for findDupes |
| getGCcontent | Get the GC content of every contig in a FASTA. |
| getHugoCache | HUGO transcript and gene names for ENSEMBL IDs of the... |
| getMostRecentCacheBuild | Indicate what the most recent ENSEMBL build is that we have... |
| getReactomeCache | Pulling Reactome mappings through biomaRt takes time. So we... |
| getReactomeUrl | Function that lets us avoid storing a redundant pile of URLs... |
| hugoCache | A list of HUGO Gene Symbols and associated ENSEMBL... |
| indexIfNoneFound | helper function for findDupes |
| loadReactome | this function should only ever be used to reload/maintain... |
| makeArrayControlLitePkg | create a ArrayControlDbLite package from sqlite file (usually... |
| makeEnsDbLitePkg | create an EnsDbLite package from sqlite file (usually via... |
| makeErccDbLitePkg | create a ErccDbLite package from sqlite file (usually via... |
| makeRepDbLitePkg | create a RepDbLite package from sqlite file (usually via... |
| mapHugo | map genes or transcripts to updated HUGO symbols |
| mapReactomeSets | this creates a reactomePathway set in terms of gene names... |
| mapToReactome | map transcripts or genes to Reactome pathways, using a cache... |
| mouse_repeat_biotypes | A Data frame of repetitive elements relating to Mus Musculus |
| reactomeCache | A list of ENSEMBL Transcripts and associated Reactome Pathway... |
| reactomePathways | A list of Reactome IDs and associated names for each reactome... |
| reactomeSets | using the cached Reactome databases, generate gene sets for... |
| RepDbLite | Constructor for an RepDbLite object. |
| repDbLiteFromFasta | functions to create a RepDbLite object (a stripped-down... |
| repDbLiteFromMouseFasta | functions to create a RepDbLite object (a stripped-down... |
| repDbLiteMetadata | create metadata for a RepDbLite instance |
| repeat_biotypes | A Data frame of repetitive elements relating to Homo Sapiens |
| spikeinDbLiteFromFasta | create an general spike in annotation DB from the FASTA file... |
| str2vec | array-ify a string with a possible leading path/URL/whatever |
| strpop | Pop a string off of a string, for (e.g.) grabbing source... |
| strpush | The opposite of strpop: push string(s) onto a string. unlike... |
| strshift | grab the first (or z'th) element(s) of x after splitting it... |
| strunshift | shove new element(s) x onto a (possibly splittable on y)... |
| supportedOrganismsForTxDbLite | A Data Frame of all supported organisms and supported... |
| TxDbLite | Create a TxDbLite object (usually called by subclass... |
| TxDbLite-class | A parent class for lightweight Ensembl and... |
| unannotatedTranscript | GRanges object for entries without annotations |
| utils | utility functions |
