convertToGRanges {InterMineR} | R Documentation

## Convert InterMineR retrieved genomic information to objects of class `GRanges`

### Description

`convertToGRanges` constitutes a wrapper function for converting genomic locations and their respective annotations to objects of the `GRanges` class.

### Usage

    convertToGRanges(
      dataset,
      seqnames,
      start,
      end,
      names,
      strand,
      columnsAsMetadata = NULL,
      listAsMetadata = NULL,
      seqnamesInterMineChromosome = TRUE
    )

### Arguments

`dataset` | a data.frame containing all the genomic information retrieved by InterMineR. Its columns are used to create the `GRanges` object.
`seqnames` | the name of a column from dataset or a character vector of length equal to the number of rows of the dataset. Defines the values assigned as seqnames to the `GRanges` object.
`start` | the name of a column from dataset or a vector of length equal to the number of rows of the dataset. Defines the genomic coordinates assigned as start to the ranges argument of the `GRanges` object.
`end` | the name of a column from dataset or a vector of length equal to the number of rows of the dataset. Defines the genomic coordinates assigned as end to the ranges argument of the `GRanges` object.
`names` | the name of a column from dataset or a character vector of length equal to the number of rows of the dataset. Defines the values assigned as names to the ranges argument of the `GRanges` object.
`strand` | the name of a column from dataset or a character vector of length equal to the number of rows of the dataset. Defines the values assigned as strand information to the `GRanges` object.
`columnsAsMetadata` | a character vector containing the names of the dataset columns that are passed as metadata in the `GRanges` object.
`listAsMetadata` | a list of vectors, each of which has length equal to the number of rows of the dataset. The values of the list are passed as metadata to the `GRanges` object.
`seqnamesInterMineChromosome` | a logical value indicating whether the values passed as seqnames are InterMineR chromosome.primaryIdentifiers (e.g. "2R", "3R", "X") or not.

### Details

The InterMineR package provides a flexible interface to the InterMine web services, which allow for rapid retrieval of various genomic information.

`convertToGRanges` function is designed to facilitate the conversion of genomic locations and their respective annotations, in the format by which they are retrieved using InterMineR, to an object of the `GRanges` class.

### Value

An object of the `GRanges` class containing genomic locations and annotations retrieved by InterMineR queries.

### Author(s)

InterMine Team

### See Also

`GRanges`, `convertToRangedSummarizedExperiment`

### Examples

    # get FlyMine
    im.fly = initInterMine(listMines()["FlyMine"])

    # modify template query for Transcription Factor (TF) Binding sites
    qTF_Binding = getTemplateQuery(im.fly,"ChromLocation_TFBindingSiteLocationGeneFactor")

    qTF_Binding$where[[4]]$value = "1000000"
    qTF_Binding$where[[5]]$value = "20000000"

    rTF_Binding = runQuery(im.fly, qTF_Binding)

    # assign random values for strand of the genomic location retrieved, in InterMine format
    rTF_Binding$gene.strand = sample(c("1", "-1", ""), nrow(rTF_Binding), replace = TRUE)

    # convert to GRanges object
    test = convertToGRanges(
      dataset = rTF_Binding,
      seqnames = rTF_Binding$TFBindingSite.chromosome.primaryIdentifier,
      names = rTF_Binding$TFBindingSite.factor.name,
      start = rTF_Binding$TFBindingSite.chromosomeLocation.start,
      end = rTF_Binding$TFBindingSite.chromosomeLocation.end,
      strand = "gene.strand",
      columnsAsMetadata = c(
        "TFBindingSite.gene.regulatoryRegions.dataSets.dataSource.name",
        "TFBindingSite.factor.primaryIdentifier"),
      listAsMetadata = list(
        c(factor.primaryIdentifier = rTF_Binding$TFBindingSite.factor.primaryIdentifier)
      )
    )

    # check results
    test

[Package InterMineR version 1.4.1 Index]