CTSS-class: CAGE Transcription Start Sites

In charles-plessy/CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

CAGE Transcription Start Sites

Description

The CTSS class represents CAGE transcription start sites (CTSS) at single-nucleotide resolution, using GenomicRanges::UnstitchedGPos as base class. It is used by CAGEr for type safety.

The CTSS constructor takes the same arguments as GenomicRanges::GPos, plus bsgenomeName, and minus stitch, which is hardcoded to FALSE.

The CTSS.chr class represents a CTSS object that is guaranteed to be only on a single chromosome. It is used internally by CAGEr for type-safe polymorphic dispatch.

Usage

## S4 method for signature 'CTSS'
show(object)

## S4 method for signature 'CTSS'
initialize(.Object, ..., bsgenomeName = NULL)

CTSS(
  seqnames = NULL,
  pos = NULL,
  strand = NULL,
  ...,
  seqinfo = NULL,
  seqlengths = NULL,
  bsgenomeName = NULL
)

## S4 method for signature 'CTSS,GRanges'
coerce(from, to = "GRanges", strict = TRUE)

## S4 method for signature 'GRanges,CTSS'
coerce(from, to = "CTSS", strict = TRUE)

Arguments

object	See methods::show
.Object	See methods::new
bsgenomeName	String containing the name of a BSgenome package.
seqnames, pos, strand, seqinfo, seqlengths, ...	See the documentation of GenomicRanges::GPos for further details.
from, to, strict	See methods::coerce.

Details

The genomeName element of the metadata slot is used to store the name of the BSgenome package used when constructing the CAGEr object.

Coercion from GRanges to CTSS loses information, but it seems to be fine, since other coercions like as(1.2, "integer") do the same.

Author(s)

Charles Plessy

Examples

# Convert an UnstitchedGPos object using the new() constructor.
gp <- GPos("chr1:2:-", stitch = FALSE)
ctss <- new("CTSS", gp, bsgenomeName = "BSgenome.Drerio.UCSC.danRer7")
genomeName(ctss)

# Create a new object using the CTSS() constructor.
CTSS("chr1", 2, "-", bsgenomeName = "BSgenome.Drerio.UCSC.danRer7")

# Coerce CTSS to GRanges
as(ctss, "GRanges")

# Coerce a GRanges object to CTSS using the as() method.
gr <- GRanges("chr1:1-10:-")
gr$seq <- "AAAAAAAAAA"
seqlengths(gr) <- 100
genome(gr) <- "foo"
as(gr, "CTSS")
identical(seqinfo(gr), seqinfo(as(gr, "CTSS")))
as(as(gr, "CTSS"), "CTSS") # Make sure it works twice in a row

# (internal use) Transform CTSS to CTSS.chr object
ctss.chr <- as(CTSScoordinatesGR(exampleCAGEexp), "CTSS.chr")

charles-plessy/CAGEr documentation built on Nov. 4, 2023, 11:57 a.m.