# Functional Annotation of Custom Transcriptomes

## Documentation for package ‘factR’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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; e.g. "chr1" vs "1") across multiple objects
importFASTA | Import FASTA file into R
importGTF | Import GTF file into R
matchChromosomes | Match seqlevels of input GRanges to reference GRanges or BioString objects
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 GenomicRangesList
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 gene
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 of the same gene
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.