"FeatComp"FeatComp-class.RdComparing feature names of two comparable MSnSet instances.
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.
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.
Accessors names, common, unique1 and
unique2 can be used to access the respective FeatComp
slots.
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).
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.
signature(object = "FeatComp"): prints a summary
of the object.
averageMSnSet to compuate an average MSnSet.
library("pRolocdata")
#>
#> This is pRolocdata version 1.41.0.
#> Use 'pRolocdata()' to list available data sets.
data(tan2009r1)
data(tan2009r2)
x <- compfnames(tan2009r1, tan2009r2)
x[[1]]
#> Object of class "FeatComp", 'all' features:
#> Common feature: 551
#> Unique to 1: 337
#> Unique to 2: 320
x[2:3]
#> [[1]]
#> Object of class "FeatComp", 'unknown' features:
#> Common feature: 413
#> Unique to 1: 264
#> Unique to 2: 331
#>
#> [[2]]
#> Object of class "FeatComp", 'ER' features:
#> Common feature: 21
#> Unique to 1: 7
#> Unique to 2: 0
#>
head(common(x[[1]]))
#> [1] "P20353" "P53501" "Q7KU78" "P04412" "Q7JZN0" "Q9VM65"
data(tan2009r3)
tanl <- list(tan2009r1, tan2009r2, tan2009r3)
xx <- compfnames(tanl, fcol1 = NULL)
length(xx)
#> [1] 15
tail(xx)
#> $`1v3`
#> Object of class "FeatComp", 'all' features:
#> Common feature: 494
#> Unique to 1: 394
#> Unique to 2: 176
#>
#> $`1v2`
#> Object of class "FeatComp", 'all' features:
#> Common feature: 551
#> Unique to 1: 337
#> Unique to 2: 320
#>
#> $`1v3`
#> Object of class "FeatComp", 'all' features:
#> Common feature: 494
#> Unique to 1: 394
#> Unique to 2: 176
#>
#> $`3v2`
#> Object of class "FeatComp", 'all' features:
#> Common feature: 477
#> Unique to 1: 193
#> Unique to 2: 394
#>
#> $`3v3`
#> Object of class "FeatComp", 'all' features:
#> Common feature: 670
#> Unique to 1: 0
#> Unique to 2: 0
#>
#> $`2v3`
#> Object of class "FeatComp", 'all' features:
#> Common feature: 477
#> Unique to 1: 394
#> Unique to 2: 193
#>
all.equal(xx[[15]],
compfnames(tan2009r2, tan2009r3, fcol1 = NULL))
#> [1] TRUE
str(sapply(xx, common))
#> List of 15
#> $ 1v2: chr [1:551] "P20353" "P53501" "Q7KU78" "P04412" ...
#> $ 1v1: chr [1:888] "P20353" "P53501" "Q7KU78" "P04412" ...
#> $ 1v3: chr [1:494] "Q7KU78" "Q7JZN0" "P15348" "Q00174" ...
#> $ 1v2: chr [1:551] "P20353" "P53501" "Q7KU78" "P04412" ...
#> $ 1v3: chr [1:494] "Q7KU78" "Q7JZN0" "P15348" "Q00174" ...
#> $ 2v1: chr [1:551] "P20353" "P53501" "Q7KU78" "P04412" ...
#> $ 2v3: chr [1:477] "Q7KU78" "Q7JZN0" "Q9VJ80" "P15348" ...
#> $ 2v2: chr [1:871] "P20432" "P20353" "P53501" "Q7KU78" ...
#> $ 2v3: chr [1:477] "Q7KU78" "Q7JZN0" "Q9VJ80" "P15348" ...
#> $ 1v3: chr [1:494] "Q7KU78" "Q7JZN0" "P15348" "Q00174" ...
#> $ 1v2: chr [1:551] "P20353" "P53501" "Q7KU78" "P04412" ...
#> $ 1v3: chr [1:494] "Q7KU78" "Q7JZN0" "P15348" "Q00174" ...
#> $ 3v2: chr [1:477] "Q7KU78" "Q7JZN0" "Q9VJ80" "P15348" ...
#> $ 3v3: chr [1:670] "Q7KU78" "Q7JZN0" "M9PC85" "Q9VJ80" ...
#> $ 2v3: chr [1:477] "Q7KU78" "Q7JZN0" "Q9VJ80" "P15348" ...