FeatComp-class {MSnbase} | R Documentation

## Class `"FeatComp"`

### Description

Comparing feature names of two comparable `MSnSet` instances.

### Objects from the Class

Objects can be created with `compfnames`. The method compares the feature names of two objects of class `"MSnSet"`. It prints a summary matrix of common and unique feature names and invisibly returns a list of `FeatComp` instances.

The function will compute the common and unique features for all feature names of the two input objects (`featureNames(x)` and `feautreNames(y)`) as well as distinct subsets as defined in the `fcol1` and `fcol2` feautre variables.

### Slots

`name`:

  Object of class `"character"` defining the name of the compared features. By convention, `"all"` is used when all feature names are used; otherwise, the respective levels of the feature variables `fcol1` and `fcol2`.

`common`:

  Object of class `"character"` with the common feature names.

`unique1`:

  Object of class `"character"` with the features unique to the first `MSnSet` (`x` in `compfname`).

`unique2`:

  Object of class `"character"` with the features unique to the seconn `MSnSet` (`y` in `compfname`).

`all`:

  Object of class `"logical"` defining if all features of only a subset were compared. One expects that `name == "all"` when `all` is `TRUE`.

### Methods

Accessors `names`, `common`, `unique1` and `unique2` can be used to access the respective `FeatComp` slots.

compfnames

  `signature(x = "MSnSet", y = "MSnSet", fcol1 = "character", fcol2 = "character", simplify = "logical", verbose = "logical")`: creates the `FeatComp` comparison object for instances `x` and `y`. The feature variables to be considered to details feature comparison can be defined by `fcol1` (default is `"markers"` and `fcol2` for `x` and `y` respectively). Setting either to `NULL` will only consider all feature names; in such case, of `simplify` is `TRUE` (default), an `FeatComp` object is returned instead of a list of length 1. The `verbose` logical controls if a summary table needs to be printed (default is `TRUE`).

compfnames

  `signature(x = "list", y = "missing", ...)`: when `x` is a list of `MSnSet` instances, `compfnames` is applied to all element pairs of `x`. Additional parameters `fcol1`, `fcol2`, `simplify` and `verbose` are passed to the pairwise comparison method.

show

  `signature(object = "FeatComp")`: prints a summary of the `object`.

### Author(s)

Laurent Gatto <lg390@cam.ac.uk> and Thomas Naake

### See Also

`averageMSnSet` to compuate an average `MSnSet`.

### Examples

    library("pRolocdata")
    data(tan2009r1)
    data(tan2009r2)
    x <- compfnames(tan2009r1, tan2009r2)
    x[[1]]
    x[2:3]
    head(common(x[[1]]))

    data(tan2009r3)
    tanl <- list(tan2009r1, tan2009r2, tan2009r3)
    xx <- compfnames(tanl, fcol1 = NULL)
    length(xx)
    tail(xx)

    all.equal(xx[[15]],
              compfnames(tan2009r2, tan2009r3, fcol1 = NULL))
    str(sapply(xx, common))

[Package MSnbase version 2.18.0 Index]