Man pages for VladaMilch/pdProbeRemap
What the package does (short line)
| Alignments | The Alignments class |
| alignments2parsedData | What function does (short) |
| alignments2probesetsRaw | What function does (short) |
| Alignments_class_example | Example of an object of class 'Alignments' |
| annotate.G.alignment | annotates probes genomic alignment |
| annotate.non25M.genomic.transcrits_wise | Map non-25M genomic mapppings to transcripts coordinates |
| annotate.T.alignment | annotate Transcriptomic Alignment data.frame |
| annotation2fasta | write probes in FASTA |
| Annotation_example | Example of an annotation 'data.frame' |
| build_new_ParsedDataOld_object_PGF | build new ParsedDataOld object PGF or CDF |
| cigar2_left | cigar - to - length of the left exon mapping |
| cigar2length | CIGAR-to-length |
| cigar2_right | cigar - to - length of the right exon mapping |
| cleanProbeSets | filter out small probe sets |
| filter.T.alignment | filter out non-unique transcriptomic mappings |
| getExonExonBorder | What function does (short) |
| makeNewAnnotationPackage | What function does (short) |
| make_objects_for_reannotation | Converts ProbeSets to package building input |
| makeOriginalPackageObject | make original annotation object |
| processAlignments | Read probe alignments from a directory |
| read.sam | Read SAM files. |
| seed_example | Example of an object used for annotation package building |
| star.command.make | generate command for STAR aligner |
