GenomicFiles: GenomicFiles objects

Description

The GenomicFiles class is a matrix-like container where rows represent ranges of interest and columns represent files. The class is designed for byFile or byRange queries and can be thought of as a precursor (or skeleton) of the SummarizedExperiment class.

GenomicFiles has slots for files, rowData, colData and exptData. Unlike SummarizedExperiment, GenomicFiles does not contain an assays slot.

Arguments

Constructor

: GenomicFiles(rowData, files, colData=DataFrame(), exptData=SimpleList(), ...):

Accessors

In the code below, x is a GenomicFiles object.

rowRanges, rowRanges(x) <- value: Get or set the rowData on x. value can be a GRanges or GRangesList representing ranges or indices defined on the spaces (position) of the files.
files(x), files(x) <- value: Get or set the files on x. value can be a character() of file paths or a List of file objects such as BamFile, BigWigFile, FaFile, etc.
colData, colData(x) <- value: Get or set the colData on x. value must be a DataFrame instance describing the files. The number of rows must match the number of files. Row names, if present, become the column names of the GenomicFiles.
exptData, exptData(x) <- value: Get or set the exptData on x. value must be a SimpleList of arbitrary content describing the overall experiment.
dimnames, dimnames(x) <- value: Get or set the row and column names on x.

Methods

In the code below, x is a GenomicFiles object.

[: Subset the object by fileRange or fileSample.
show: Compactly display the object.
reduceByFile: Extract, manipulate and combine data defined in rowData within the files specified in files. See ?reduceByFile for details.
reduceByRange: Extract, manipulate and combine data defined in rowData across the files specified in files. See ?reduceByRange for details.

Examples

Run this code

if (require(RNAseqData.HNRNPC.bam.chr14)) { 
  fl <- RNAseqData.HNRNPC.bam.chr14_BAMFILES
  rd <- GRanges("chr14", 
                 IRanges(c(62262735, 63121531, 63980327), width=214700))
  cd <- DataFrame(method=rep("RNASeq", length(fl)),
                  format=rep("bam", length(fl)))

  ## Construct an instance of the class:
  gf <- GenomicFiles(files = fl, rowData = rd, colData = cd) 
  gf

  ## Subset on ranges or files for different experimental runs.
  dim(gf)
  gf_sub <- gf[2, 3:4]
  dim(gf_sub)
 
  ## When summarize = TRUE and no REDUCE is provided the reduceBy* 
  ## functions output a SummarizedExperiment object.
  MAP <- function(range, file, ...) {
      library(GenomicRanges) ## for coverage()
      library(Rsamtools)     ## for ScanBamParam()
      param = ScanBamParam(which=range)
      coverage(file, param=param)[range]
  } 
  se <- reduceByRange(gf, MAP=MAP, summarize=TRUE)
  se
 
  ## Data from the rowData, colData and exptData slots in the
  ## GenomicFiles are transferred to the SummarizedExperiment.
  colData(se)
 
  ## Results are in the assays slot.
  assays(se) 
}