Functional Annotation of Custom Transcriptomes

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Documentation for package ‘factR’ version 1.2.0

• 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.