slots {SGSeq} | R Documentation

## Accessing and replacing metadata columns

### Description

Accessor and replacement functions for metadata columns.

### Usage

    type(x) <- value

    txName(x)

    txName(x) <- value

    geneName(x)

    geneName(x) <- value

    featureID(x)

    featureID(x) <- value

    geneID(x)

    geneID(x) <- value

    splice5p(x)

    splice5p(x) <- value

    splice3p(x)

    splice3p(x) <- value

    from(x) <- value

    to(x) <- value

    segmentID(x)

    segmentID(x) <- value

    variantID(x)

    variantID(x) <- value

    eventID(x)

    eventID(x) <- value

    closed5p(x)

    closed5p(x) <- value

    closed3p(x)

    closed3p(x) <- value

    closed5pEvent(x)

    closed5pEvent(x) <- value

    closed3pEvent(x)

    closed3pEvent(x) <- value

    variantType(x)

    variantType(x) <- value

    variantName(x)

    variantName(x) <- value

    featureID5p(x)

    featureID5p(x) <- value

    featureID3p(x)

    featureID3p(x) <- value

    featureID5pEvent(x)

    featureID5pEvent(x) <- value

    featureID3pEvent(x)

    featureID3pEvent(x) <- value

    ## S4 method for signature 'Features'
    type(x)

    ## S4 method for signature 'Paths'
    type(x)

    ## S4 method for signature 'Counts'
    type(x)

    ## S4 replacement method for signature 'Features'
    type(x) <- value

    ## S4 replacement method for signature 'Paths'
    type(x) <- value

    ## S4 replacement method for signature 'Counts'
    type(x) <- value

    ## S4 method for signature 'Features'
    txName(x)

    ## S4 method for signature 'Paths'
    txName(x)

    ## S4 method for signature 'Counts'
    txName(x)

    ## S4 replacement method for signature 'Features'
    txName(x) <- value

    ## S4 replacement method for signature 'Paths'
    txName(x) <- value

    ## S4 replacement method for signature 'Counts'
    txName(x) <- value

    ## S4 method for signature 'Features'
    geneName(x)

    ## S4 method for signature 'Paths'
    geneName(x)

    ## S4 method for signature 'Counts'
    geneName(x)

    ## S4 replacement method for signature 'Features'
    geneName(x) <- value

    ## S4 replacement method for signature 'Paths'
    geneName(x) <- value

    ## S4 replacement method for signature 'Counts'
    geneName(x) <- value

    ## S4 method for signature 'SGFeatures'
    featureID(x)

    ## S4 method for signature 'Paths'
    featureID(x)

    ## S4 method for signature 'Counts'
    featureID(x)

    ## S4 replacement method for signature 'SGFeatures'
    featureID(x) <- value

    ## S4 replacement method for signature 'Paths'
    featureID(x) <- value

    ## S4 replacement method for signature 'Counts'
    featureID(x) <- value

    ## S4 method for signature 'SGFeatures'
    geneID(x)

    ## S4 method for signature 'Paths'
    geneID(x)

    ## S4 method for signature 'Counts'
    geneID(x)

    ## S4 replacement method for signature 'SGFeatures'
    geneID(x) <- value

    ## S4 replacement method for signature 'Paths'
    geneID(x) <- value

    ## S4 replacement method for signature 'Counts'
    geneID(x) <- value

    ## S4 method for signature 'SGFeatures'
    splice5p(x)

    ## S4 method for signature 'SGSegments'
    splice5p(x)

    ## S4 method for signature 'SGFeatureCounts'
    splice5p(x)

    ## S4 replacement method for signature 'SGFeatures'
    splice5p(x) <- value

    ## S4 replacement method for signature 'SGSegments'
    splice5p(x) <- value

    ## S4 replacement method for signature 'SGFeatureCounts'
    splice5p(x) <- value

    ## S4 method for signature 'SGFeatures'
    splice3p(x)

    ## S4 method for signature 'SGSegments'
    splice3p(x)

    ## S4 method for signature 'SGFeatureCounts'
    splice3p(x)

    ## S4 replacement method for signature 'SGFeatures'
    splice3p(x) <- value

    ## S4 replacement method for signature 'SGSegments'
    splice3p(x) <- value

    ## S4 replacement method for signature 'SGFeatureCounts'
    splice3p(x) <- value

    ## S4 method for signature 'Paths'
    segmentID(x)

    ## S4 method for signature 'SGVariantCounts'
    segmentID(x)

    ## S4 replacement method for signature 'Paths'
    segmentID(x) <- value

    ## S4 replacement method for signature 'SGVariantCounts'
    segmentID(x) <- value

    ## S4 method for signature 'Paths'
    from(x)

    ## S4 method for signature 'SGVariantCounts'
    from(x)

    ## S4 replacement method for signature 'Paths'
    from(x) <- value

    ## S4 replacement method for signature 'SGVariantCounts'
    from(x) <- value

    ## S4 method for signature 'Paths'
    to(x)

    ## S4 method for signature 'SGVariantCounts'
    to(x)

    ## S4 replacement method for signature 'Paths'
    to(x) <- value

    ## S4 replacement method for signature 'SGVariantCounts'
    to(x) <- value

    ## S4 method for signature 'SGVariants'
    eventID(x)

    ## S4 method for signature 'SGVariantCounts'
    eventID(x)

    ## S4 replacement method for signature 'SGVariants'
    eventID(x) <- value

    ## S4 replacement method for signature 'SGVariantCounts'
    eventID(x) <- value

    ## S4 method for signature 'SGVariants'
    variantID(x)

    ## S4 method for signature 'SGVariantCounts'
    variantID(x)

    ## S4 replacement method for signature 'SGVariants'
    variantID(x) <- value

    ## S4 replacement method for signature 'SGVariantCounts'
    variantID(x) <- value

    ## S4 method for signature 'SGVariants'
    closed5p(x)

    ## S4 method for signature 'SGVariantCounts'
    closed5p(x)

    ## S4 replacement method for signature 'SGVariants'
    closed5p(x) <- value

    ## S4 replacement method for signature 'SGVariantCounts'
    closed5p(x) <- value

    ## S4 method for signature 'SGVariants'
    closed3p(x)

    ## S4 method for signature 'SGVariantCounts'
    closed3p(x)

    ## S4 replacement method for signature 'SGVariants'
    closed3p(x) <- value

    ## S4 replacement method for signature 'SGVariantCounts'
    closed3p(x) <- value

    ## S4 method for signature 'SGVariants'
    closed5pEvent(x)

    ## S4 method for signature 'SGVariantCounts'
    closed5pEvent(x)

    ## S4 replacement method for signature 'SGVariants'
    closed5pEvent(x) <- value

    ## S4 replacement method for signature 'SGVariantCounts'
    closed5pEvent(x) <- value

    ## S4 method for signature 'SGVariants'
    closed3pEvent(x)

    ## S4 method for signature 'SGVariantCounts'
    closed3pEvent(x)

    ## S4 replacement method for signature 'SGVariants'
    closed3pEvent(x) <- value

    ## S4 replacement method for signature 'SGVariantCounts'
    closed3pEvent(x) <- value

    ## S4 method for signature 'SGVariants'
    variantName(x)

    ## S4 method for signature 'SGVariantCounts'
    variantName(x)

    ## S4 replacement method for signature 'SGVariants'
    variantName(x) <- value

    ## S4 replacement method for signature 'SGVariantCounts'
    variantName(x) <- value

    ## S4 method for signature 'SGVariants'
    variantType(x)

    ## S4 method for signature 'SGVariantCounts'
    variantType(x)

    ## S4 replacement method for signature 'SGVariants'
    variantType(x) <- value

    ## S4 replacement method for signature 'SGVariantCounts'
    variantType(x) <- value

    ## S4 method for signature 'SGVariants'
    featureID5p(x)

    ## S4 method for signature 'SGVariantCounts'
    featureID5p(x)

    ## S4 replacement method for signature 'SGVariants'
    featureID5p(x) <- value

    ## S4 replacement method for signature 'SGVariantCounts'
    featureID5p(x) <- value

    ## S4 method for signature 'SGVariants'
    featureID3p(x)

    ## S4 method for signature 'SGVariantCounts'
    featureID3p(x)

    ## S4 replacement method for signature 'SGVariants'
    featureID3p(x) <- value

    ## S4 replacement method for signature 'SGVariantCounts'
    featureID3p(x) <- value

    ## S4 method for signature 'SGVariants'
    featureID5pEvent(x)

    ## S4 method for signature 'SGVariantCounts'
    featureID5pEvent(x)

    ## S4 replacement method for signature 'SGVariants'
    featureID5pEvent(x) <- value

    ## S4 replacement method for signature 'SGVariantCounts'
    featureID5pEvent(x) <- value

    ## S4 method for signature 'SGVariants'
    featureID3pEvent(x)

    ## S4 method for signature 'SGVariantCounts'
    featureID3pEvent(x)

    ## S4 replacement method for signature 'SGVariants'
    featureID3pEvent(x) <- value

    ## S4 replacement method for signature 'SGVariantCounts'
    featureID3pEvent(x) <- value

### Arguments

`x` | Object containing metadata column
`value` | Replacement value

### Details

S4 classes defined in the `SGSeq` package contain metadata columns that store information for each element in the object. For example, class `TxFeatures` contains a column `type` that indicates feature type. The specific columns contained in an object depend on its class.

### Value

Content of metadata column for accessor functions or updated object for replacement functions.

### Author(s)

Leonard Goldstein

### Examples

    head(type(txf_ann))
    head(type(sgf_ann))

[Package SGSeq version 1.28.0 Index]