generateGenicElementCoor: Function processes UCSC genePred tables to generate coordinates for various genic elements like introns, exons, CDS, UTRs, and upstream and downstream regions. It handles these coordinates with consideration for strand sensitivity and genome information.

Description

All the operations in here are vectorized. If the table is big, expect a spike in memory. Using ncbiRefSeq table and genome hg38, the memory is stable at 4-5 GB. I can utilise data.table package to process by chunk if needed. Original table is zero-based open-end index. The indexing system is changed temporarily to follow Rs system. The output coordinate table is one-based close-end index. Critical information based on UCSC Genome website: Column Explanation bin Indexing field to speed chromosome range queries. (Only relevant to UCSC program) name Name of gene (usually transcript_id from GTF) chrom Reference sequence chromosome or scaffold strand + or - for strand txStart Transcription start position (or end position for minus strand item) txEnd Transcription end position (or start position for minus strand item) cdsStart Coding region start (or end position for minus strand item) cdsEnd Coding region end (or start position for minus strand item) exonCount Number of exons exonEnds Exon end positions (or start positions for minus strand item) exonStart Exon start positions (or end positions for minus strand item) name2 Alternate name (e.g. gene_id from GTF) cdsStartStat Status of CDS start annotation (none, unknown, incomplete, or complete) = ('none','unk','incmpl','cmpl') cdsEndStat Status of CDS end annotation (none, unknown, incomplete, or complete) exonFrames Exon frame (0,1,2), or -1 if no frame for exon (Related to codon. Number represents extra bases (modulus of 3) from previous exon block brought to a current exon block.) If cdsStart == cdsEnd, that means non-coding sequence.

maybe cdsStartStat and cdsEndStat == "none" mean the same thing. maybe exonFrames == "-1," means the same thing.

Usage

generateGenicElementCoor(
  genepred,
  element.names = "all",
  upstream = NULL,
  downstream = NULL,
  genome.name = NULL,
  genome = NULL,
  return.coor.obj = FALSE
)

Value

Genic element coordinates in a data.table or Coordinate object.

Arguments

genepred: UCSC genome name (e.g., hg19, mm39).
element.names: Types of genic elements to output: "all", "intron", "exon", "CDS", or "UTR". Default is "all".
upstream: Length of upstream sequence (can overlap other genes).
downstream: Length of downstream sequence (can overlap other genes).
genome.name: UCSC genome name for trimming overflowing coordinates.
genome: Genome object for coordinate resolution.
return.coor.obj: Whether to return a Coordinate object (default: FALSE).