aGFF-class: Class for storing GFF-like data

In ACME: Algorithms for Calculating Microarray Enrichment (ACME)

Description

The GFF format is quite versatile while remaining simple. This class simply stores the annotation associated with a set of GFF files from the same regions of the genome along with some information about the samples from which the data came and the data (from the "score" column of the GFF file) themselves.

Objects from the Class

Objects can be created by calls of the form new("aGFF", ...). Also, the read.resultsGFF() function returns aGFF objects.

Slots

annotation:

Object of class "data.frame" with two columns absolutely necessary, "Chromosome" and "Location". Other columns can be included.

data:

Object of class "matrix" of the same number of rows as the annotation slot and the same number of columns as the number of rows in the samples slot, containing data for later analysis

samples:

Object of class "data.frame" for describing the samples, one row per sample

Methods

plot

signature(x = "aGFF"): to plot a region along the genome.

print

signature(x = "aGFF"): simple method to display summary of aGFF object

show

signature(object = "aGFF"): simple method to display summary of aGFF object

Author(s)

Sean Davis

See Also

read.resultsGFF andaGFFCalc-class

Examples

# Load an example
data(example.agff)
example.agff

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

ACMESet (storageMode: lockedEnvironment)
assayData: 190181 features, 2 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: testsamp1 testsamp2
  varLabels: fullfnames
  varMetadata: labelDescription
featureData
  featureNames: 74065 74066 ... 103913 (190181 total)
  fvarLabels: chromosome source ... comment (8 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  

ACME documentation built on Nov. 8, 2020, 7:51 p.m.