R: Yeast gene model sample data

sgd {intervals} | R Documentation

## Yeast gene model sample data

### Description

This data set contains a data frame describing a subset of the chromosome feature data represented in Fall 2007 version of ‘saccharomyces\_cerevisiae.gff’, available for download from the Saccharomyces Genome Database (http://www.yeastgenome.org).

### Usage

    data(sgd)

### Format

A data frame with 14080 observations on the following 8 variables.

`SGDID`

  SGD feature ID.

`type`

  Only four feature types have been retatined: `"CDS"`, `"five_prime_UTR_intron"`, `"intron"`, and `"ORF"`. Note that `"ORF"` correspond to a whole gene while `"CDS"`, to an exon. S. cerevisae does not, however, have many multi-exonic genes.

`feature_name`

  A character vector

`parent_feature_name`

  The `feature_name` of the a larger element to which the current feature belongs. All retained `"CDS"` entries, for example, belong to an `"ORF"` entry.

`chr`

  The chromosome on which the feature occurs.

`start`

  Feature start base.

`stop`

  Feature stop base.

`strand`

  Is the feature on the Watson or Crick strand?

### Examples

    # An example to compute "promoters", defined to be the 500 bases
    # upstream from an ORF annotation, provided these bases don't intersect
    # another orf. See documentation for the sgd data set for more details
    # on the annotation set.

    use_chr <- "chr01"

    data( sgd )
    sgd <- subset( sgd, chr == use_chr )

    orf <- Intervals(
                     subset( sgd, type == "ORF", c( "start", "stop" ) ),
                     type = "Z"
                     )
    rownames( orf ) <- subset( sgd, type == "ORF" )$feature_name

    W <- subset( sgd, type == "ORF", "strand" ) == "W"

    promoters_W <- Intervals(
                             cbind( orf[W,1] - 500, orf[W,1] - 1 ),
                             type = "Z"
                             )

    promoters_W <- interval_intersection(
                                         promoters_W,
                                         interval_complement( orf )
                                         )

    # Many Watson-strand genes have another ORF upstream at a distance of
    # less than 500 bp

    hist( size( promoters_W ) )

    # All CDS entries are completely within their corresponding ORF entry.

    cds_W <- Intervals(
                     subset( sgd, type == "CDS" & strand == "W", c( "start", "stop" ) ),
                     type = "Z"
                     )
    rownames( cds_W ) <- NULL

    interval_intersection( cds_W, interval_complement( orf[W,] ) )

[Package intervals version 0.15.2 Index]