Reference

All functions

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

matchGeneInfo()

Match gene metadata from query GTF to a reference GTF

matched_query_gtf

Seqlevels and gene_id matched query data

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.