tidySet.GeneSetCollection | R Documentation |
These functions help to create a TidySet
object from
data.frame
, list
, matrix
, and GO3AnnDbBimap
.
They can create both fuzzy and standard sets.
## S3 method for class 'GeneSetCollection'
tidySet(relations)
## S3 method for class 'GeneColorSet'
tidySet(relations)
## S3 method for class 'GeneSet'
tidySet(relations)
tidySet(relations)
## S3 method for class 'data.frame'
tidySet(relations)
## S3 method for class 'list'
tidySet(relations)
## S3 method for class 'matrix'
tidySet(relations)
## S3 method for class 'Go3AnnDbBimap'
tidySet(relations)
## S3 method for class 'TidySet'
tidySet(relations)
relations |
An object to be coerced to a TidySet. |
Elements or sets without any relation are not shown when printed.
A TidySet object.
tidySet(GeneSetCollection)
: Converts to a tidySet given a GeneSetCollection
tidySet(GeneColorSet)
: Converts to a tidySet given a GeneColorSet
tidySet(GeneSet)
: Converts to a tidySet given a GeneSet
tidySet(data.frame)
: Given the relations in a data.frame
tidySet(list)
: Convert to a TidySet from a list.
tidySet(matrix)
: Convert an incidence matrix into a TidySet
tidySet(Go3AnnDbBimap)
: Convert Go3AnnDbBimap into a TidySet object.
tidySet(TidySet)
: Convert TidySet into a TidySet object.
TidySet
# Needs GSEABase package from Bioconductor
if (requireNamespace("GSEABase", quietly = TRUE)) {
library("GSEABase")
gs <- GeneSet()
gs
tidySet(gs)
fl <- system.file("extdata", "Broad.xml", package="GSEABase")
gs2 <- getBroadSets(fl) # actually, a list of two gene sets
TS <- tidySet(gs2)
dim(TS)
sets(TS)
}
relations <- data.frame(
sets = c(rep("a", 5), "b"),
elements = letters[seq_len(6)]
)
tidySet(relations)
relations2 <- data.frame(
sets = c(rep("A", 5), "B"),
elements = letters[seq_len(6)],
fuzzy = runif(6)
)
tidySet(relations2)
# A
x <- list("A" = letters[1:5], "B" = LETTERS[3:7])
tidySet(x)
# A fuzzy set taken encoded as a list
A <- runif(5)
names(A) <- letters[1:5]
B <- runif(5)
names(B) <- letters[3:7]
relations <- list(A, B)
tidySet(relations)
# Will error
# x <- list("A" = letters[1:5], "B" = LETTERS[3:7], "c" = runif(5))
# a <- tidySet(x) # Only characters or factors are allowed as elements.
M <- matrix(c(1, 0.5, 1, 0), ncol = 2,
dimnames = list(c("A", "B"), c("a", "b")))
tidySet(M)
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