compare {RNAmodR} | R Documentation

## Comparison of Samples

### Description

To compare data of different samples, a `ModifierSet` can be used. To select the data alongside the transcripts and their positions a `GRanges` or a `GRangesList` needs to be provided. In case of a `GRanges` object, the parent column must match the transcript names as defined by the out put of `ranges(x)`, whereas in case of a `GRangesList` the element names must match the transcript names.

### Usage

    compare(x, name, pos = 1L, ...)

    compareByCoord(x, coord, ...)

    plotCompare(x, name, pos = 1L, normalize, ...)

    plotCompareByCoord(x, coord, normalize, ...)

    ## S4 method for signature 'ModifierSet'
    compare(x, name, pos = 1L, normalize, ...)

    ## S4 method for signature 'ModifierSet,GRanges'
    compareByCoord(x, coord, normalize, ...)

    ## S4 method for signature 'ModifierSet,GRangesList'
    compareByCoord(x, coord, normalize, ...)

    ## S4 method for signature 'ModifierSet'
    plotCompare(x, name, pos = 1L, normalize, ...)

    ## S4 method for signature 'ModifierSet,GRanges'
    plotCompareByCoord(x, coord, normalize, ...)

    ## S4 method for signature 'ModifierSet,GRangesList'
    plotCompareByCoord(x, coord, normalize, ...)

### Arguments

`x` | a `Modifier` or `ModifierSet` object.
`name` | Only for `compare`: the transcript name
`pos` | Only for `compare`: pos for comparison
`...` | optional parameters: `alias` a data.frame with two columns, `tx_id` and `name`, to convert transcipt ids to another identifier `name` Limit results to one specific gene or transcript `sequenceData` TRUE or FALSE? Should the aggregate of sequenceData be used for the comparison instead of the aggregate data if each `Modifier` element? (default: `sequenceData = FALSE`) `compareType` a valid score type to use for the comparison. If `sequenceData = FALSE` this defaults to `mainScore(x)`, whereas if `sequenceData = TRUE` all columns will be used by setting `allTypes = TRUE`. `allTypes` TRUE or FALSE? Should all available score be compared? (default: `allTypes = sequenceData`) ... passed on to `subsetByCoord`
`coord` | coordinates of position to subset to. Either a `GRanges` or a `GRangesList` object. For both types the 'Parent' column is expected to match the transcript name. The `GRangesList` object is unlisted and only non duplicated entries are retained.
`normalize` | either a single logical or character value. If it is a character, it must match one of the names in the `ModifierSet`.

### Value

`compareByCoord` returns a `DataFrame` and `plotCompareByCoord` returns a `ggplot` object, which can be modified further. The `DataFrame` contains columns per sample as well as the columns `names`, `positions` and `mod` incorporated from the `coord` input. If `coord` contains a column `Activity` this is included in the results as well.

### Examples

    data(msi,package="RNAmodR")
    # constructing a GRanges obejct to mark positive positions
    mod <- modifications(msi)
    coord <- unique(unlist(mod))
    coord$score <- NULL
    coord$sd <- NULL
    # return a DataFrame
    compareByCoord(msi,coord)
    # plot the comparison as a heatmap
    plotCompareByCoord(msi,coord)

[Package RNAmodR version 1.4.2 Index]