Man pages for fursham-h/factR
Functional Annotation of Custom Transcriptomes
| buildCDS | Reference-guided construction of CDS on GTF object |
| chrom_matched_query_gtf | Chromosome matched version of "query_gtf" |
| domains.known | Example output of predictDomains() |
| domains.out | Example output of predictDomains() |
| filtereach | Internally filter each element of a GenomicRangesList |
| has_consistentSeqlevels | Test consistency of chromosome naming styles (aka seqlevels;... |
| importFASTA | Import FASTA file into R |
| importGTF | Import GTF file into R |
| matchChromosomes | Match seqlevels of input GRanges to reference GRanges or... |
| matched_query_gtf | Seqlevels and gene_id matched query data |
| matchGeneInfo | Match gene metadata from query GTF to a reference GTF |
| mutateeach | Internally create or transform metadata of a... |
| new_query_gtf | Query data containing CDS information |
| predictDomains | Predict protein domain families from coding transcripts |
| predictNMD | Predict NMD sensitivity on mRNA transcripts |
| query_cds | CDS from 4 transcripts entries of the same gene |
| query_exons | GRangeList of exons from 4 transcripts entries from query_gtf |
| query_gtf | Imported GTF file containing 4 transcript entries of the same... |
| ref_cds | CDS from 2 reference transcripts entries of the same gene |
| ref_exons | Exons from 2 reference transcripts entries of the same gene |
| ref_gtf | Imported GTF file containing 2 reference transcript entries... |
| sorteach | Internally sort each element of a GenomicRangesList |
| subsetNewTranscripts | Shortlist GTF GRanges object for new transcripts |
| trimTranscripts | Resize 5' and 3' ends of a transcript GenomicRanges |
| viewTranscripts | Plot transcripts directly from GTF. |
