Man pages for malnirav/hiAnnotator
Functions for annotating GRanges objects
| cleanColname | Clean the supplied string from punctuations and spaces. |
| doAnnotation | Annotate a GRanges object using one of annotation functions. |
| dot-checkArgsSetDefaults | Check args and set defaults. |
| dot-mergeAndReturn | Merge results back to the query object and perform additional... |
| genes | Sample RefSeq genes annotation |
| get2NearestFeature | Get two nearest upstream and downstream annotation boundary... |
| getFeatureCounts | Get counts of annotation within a defined window around each... |
| getFeatureCountsBig | Get counts of annotation within a defined window around each... |
| getLowestDists | Get the lowest biological distance from the 5' or 3'... |
| getNearestFeature | Get nearest annotation boundary for a position range. |
| getRelevantCol | Find the column index of interest given the potential... |
| getSitesInFeature | Find overlapping positions/ranges that match between the... |
| getUCSCtable | Obtain a UCSC annotation table given the table & track name. |
| getWindowLabel | Generate a window size label. |
| hiAnnotator | Annotating GRanges objects with hiAnnotator. |
| makeChunks | Breaks two GRanges objects into chunks of N size. |
| makeGRanges | Make a sorted GRanges object from a dataframe. |
| makeUCSCsession | Initiate UCSC genome browser session given the freeze... |
| plotdisFeature | Plot distance distribution to a feature boundary. |
| sites | Sample Retrovirus Integration Sites data |
| sites.ctrl | Controls for Sample Retrovirus Integration Sites data |
