getCDS: Finds all genes overlapping a rearrangement (ignoring strand)...

In cancer-genomics/trellis: Somatic structural variant analysis

Finds all genes overlapping a rearrangement (ignoring strand) and returns the full CDS of each

Description

Finds all genes overlapping the linkedBins of a Rearrangement object (ignoring strand) and extracts the full CDS. The rearrangement type inferred from the position and strand orientation of read pairs (see RearrangementType) determines the orientation of the genes in the rearranged genome. See detail for the generic symbols used to denote a fused transcript.

Usage

getCDS(rear, tx, cds)

Arguments

rear	A Rearrangement object
tx	A GRanges object of transcripts from the TxDb object
cds	A GRangesList object containing the CDS for each transcript

Details

#'

Reference   (-- chr1, == chr2,  .... not in rearranged transcript)
          A                                    C
5' + ------------|.........   ...............|==============
3' - ------------|.........   ...............|==============
          B                                    D


Tumor

      chr1  A        C
5' + -------------|==========
3' - -------------|==========
            B        D

Deletions: For a deletion, we have chr1 = chr2, R1+ < R2-, and R1- > R2+. The possible fusions are AC and DB.

Translocations: A read pair in a translocation supports one of trans1, trans2, trans3, and trans4. For a balanced translocation, all four types could be observed. We analyze the data as a balanced translocation and evaluate all possible fusions even if not all types are observed. Again, the possible fusions are AC and DB.

Amplicons and translocations in which the sequences is inverted in the rearranged genome are analyzed as inversions.

Inversions: There are 8 possible fusions indicated by an inverted read pair denoted as invX, where X = 1-8. Possible fused gene products are AD, CB, BC, and DA.

Value

a Transcripts object

Examples

  options(warn=-1)
  library("TxDb.Hsapiens.UCSC.hg19.refGene")
  txdb <- TxDb.Hsapiens.UCSC.hg19.refGene
  tx <- transcripts(txdb)
  cds.all <- cdsBy(txdb, "tx", use.names=TRUE)
  data(rear_list, package="trellis")
  r <- rear_list[["18557-18736"]]
  ##data(rear_cds, package="trellis")
  ##trace(getCDS, browser)
  rear_cds <- getCDS(r, tx, cds.all)
  fusions(rear_cds)
  ## There are for transcripts for gene 'B'.  The accessor txB
  ## returns the CDSs for each of the transcripts as a
  ## \code{GRangesList}
  txB(rear_cds)
  ## Similarly, there are accessors \code{txA}, \code{txC}, and
  ## \code{txD}

cancer-genomics/trellis documentation built on Feb. 2, 2023, 7:04 p.m.