Package 'BiocSet'

BiocSet class

Description

character()

The BiocSet constructor, the show method, the slot accessors, and creating a BiocSet object from an element set tibble rather than character vector(s).

Usage

BiocSet(..., metadata = list(), active = c("elementset", "element", "set"))

## S4 method for signature 'BiocSet'
show(object)

es_element(x)

## S4 method for signature 'BiocSet'
es_element(x)

es_set(x)

## S4 method for signature 'BiocSet'
es_set(x)

es_elementset(x)

## S4 method for signature 'BiocSet'
es_elementset(x)

BiocSet_from_elementset(elementset, element, set, metadata)

Arguments

...	Named character() vectors of element sets, or a named list of character() vectors. Each character vector is an element set. The names of the character vectors are the names of the sets.
metadata	A list() with arbitrary content, describing the set.
active	A character(1) to indicate which tibble is active. The default is "elementset".
object	A BiocSet object.
x	A BiocSet object.
elementset	A tibble with element set information.
element	A tibble with element information.
set	A tibble with set information.

Value

An S4 BiocSet object shown as a tripple tibble, where each slot is a tibble.

Slots

element

The element tibble from 'tbl_elementset'

set

The set tibble from 'tbl_elementset'

elementset

The elementset tibble created from user input

active

A character(1), indicates which tibble is active

metadata

A list() with arbitrary elements describing the set

Examples

BiocSet(set1 = letters, set2 = LETTERS)
lst <- list(set1 = letters, set2 = LETTERS)
BiocSet(lst)

set.seed(123)
element <-
   tibble(
       element = letters[1:10],
       v1 = sample(10),
       v2 = sample(10)
   )
set <-
   tibble(
       set = LETTERS[1:2],
       v1 = sample(2),
       v2 = sample(2)
   )
elementset <-
   tibble(
       element = letters[1:10],
       set = sample(LETTERS[1:2], 10, TRUE)
   )
BiocSet_from_elementset(elementset, element, set)

---

as("BiocSet", "list")

Description

as("BiocSet", "list")

---

Functions applied to elements in a BiocSet object

Description

All of the major methods applied to a BiocSet object can be explicitly applied to the element tibble. These functions bypass the need to use the es_activate function by indicating what function should be used on the element tibble.

Usage

filter_element(.data, ...)

select_element(.data, ...)

mutate_element(.data, ...)

summarise_element(.data, ...)

arrange_element(.data, ...)

left_join_element(.data, ...)

tibble_from_element(.data, how = unlist)

data.frame_from_element(.data, how = unlist)

Arguments

.data	A BiocSet object.
...	Additional arguments passed to the function.
how	Multiple entries will become a list.

Value

A BiocSet object.

For tibble_from_element, a tibble.

For data.frame_from_element, a data.frame.

Examples

es <- BiocSet(set1 = letters, set2 = LETTERS)
filter_element(es, element == "a")

es %>% select_element(element)

es %>% mutate_element(pval = rnorm(1:52))

es %>% summarise_element(n = n())

es %>% arrange_element(desc(element))

tbl <- tibble(x = 1:5, y = letters[1:5])
es <- BiocSet(set1 = letters[c(1,3,5)], set2 = letters[c(2,4)])
left_join_element(es, tbl, by = c(element = "y"))

tibble_from_element(es)

data.frame_from_element(es)

---

Functions applied to elementsets in a BiocSet object

Description

All of the major methods applied to a BiocSet object can be explicitly applied to the elementset tibble. These functions bypass the need to use the es_activate function by indicating what function should be used on the elementset tibble.

Usage

filter_elementset(.data, ...)

select_elementset(.data, ...)

mutate_elementset(.data, ...)

summarise_elementset(.data, ...)

arrange_elementset(.data, ...)

left_join_elementset(.data, ...)

tibble_from_elementset(.data)

data.frame_from_elementset(.data)

Arguments

.data	A BiocSet object.
...	Additional arguments passed to the function.

Value

A BiocSet object.

For tibble_from_elementset, a tibble.

For data.frame_from_elementset, a data.frame.

Examples

es <- BiocSet(set1 = letters, set2 = LETTERS)
filter_elementset(es, element == "a" | element == "A")

es %>% select_elementset(element)

es %>% mutate_elementset(pval = rnorm(1:52))

es %>% summarise_elementset(n = n())

es %>% arrange_elementset(desc(element))

tbl <- tibble(x = 5:6, y = c("set1", "set2"))
es %>% left_join_elementset(tbl, by = c(set = "y"))

tibble_from_elementset(es)

data.frame_from_elementset(es)

---

GeneSetCollection

Description

The following functions deal with converting a BiocSet object into a GeneSetCollection object, or vice versa.

Usage

GeneSetCollection_from_BiocSet(biocset)

BiocSet_from_GeneSetCollection(gsc)

Arguments

biocset	The BiocSet object that will become a GeneSetCollection object.
gsc	The GeneSetCollection that will become a BiocSet object.

Value

For 'GeneSetCollection_from_BiocSet()', a GeneSetCollection.

For 'BiocSet_from_GeneSetCollection()', a BiocSet object.

Examples

biocset <- BiocSet(set1 = letters, set2 = LETTERS)
gsc <- GeneSetCollection_from_BiocSet(biocset)
gsc

BiocSet_from_GeneSetCollection(gsc)

---

Importing/exporting

Description

Importing/exporting and formating of element sets as a BiocSet object.

Usage

## S4 method for signature 'GMTFile,ANY,ANY'
import(con, format, text, ...)

## S4 method for signature 'BiocSet,GMTFile,ANY'
export(object, con, format, ...)

## S4 method for signature 'OBOFile,ANY,ANY'
import(con, format, text, ...)

## S4 method for signature 'BiocSet,OBOFile,ANY'
export(object, con, format, ...)

Arguments

con	For import, the file name or URL the element set is loaded from. For export, the file name or URL the element set is written to.
format	For import, the format of the input. For export, the format of the output.
text	If con is missing this is a character vector directly providing the element set that should be imported.
...	Parameters to pass to the format-specific method
object	For 'export()', the object to be exported.

Value

For 'import()', a BiocSet object

For 'export()', a GMTFile object representing the location where the BiocSet object was written to

Examples

gmtFile <- system.file(package = "BiocSet", "extdata",
    "hallmark.gene.symbol.gmt")
tbl <- import(gmtFile)

tbl2 <- BiocSet(set1 = letters, set2 = LETTERS)
fl <- tempfile(fileext = ".gmt")
gmt <- export(tbl2, fl)

oboFile <- system.file(package = "BiocSet", "extdata", "sample_go.obo")
tst_obo <- import(oboFile)
fl <- system.file("extdata", "sample_go.obo", package = "BiocSet")
tbl <- import(fl)
new_fl <- tempfile(fileext = ".obo")
obo <- export(tbl, new_fl)

---

Intersect on a single BiocSet object

Description

This function performs an intersection within a single BiocSet object.

Usage

intersect_single(x, ...)

Arguments

x	A BiocSet object.
...	Additional arguments passed to function.

Value

A BiocSet object with a single set 'intersect' and interesected elements from x.

Examples

es1 <- BiocSet(set1 = letters[c(1:10)], set2 = letters[c(4:20)])
intersect_single(es1)

---

Functions for mapping elements in the element tibble to different id types

Description

Functions for dealing with unique mapping and multiple mapping. map_add_element will add the mapping as a new column instead of overwriting the current one used for the mapping.

Usage

map_unique(es, org, from, to)

map_multiple(
  es,
  org,
  from,
  to,
  multi = c("list", "filter", "asNA", "CharacterList")
)

map_add_element(es, org, from, add)

Arguments

es	The BiocSet objec to map the elements on.
org	The AnnotationDbi object to identify keys/mappings from.
from	A character to indicate which identifier to map from.
to	A character to indicate which identifier to map to.
multi	How should multiple values be returned? Options include: list: This will just return a list object to the end user. filter: This will remove all elements that contain multiple matches and will therefore return a shorter vector than what came in whenever some of the keys match more than one value. asNA: This will return an NA value whenever there are multiple matches. CharacterList: This just returns a SimpleCharacterList object. FUN: A function can be supplied to the 'multiVals' argument for custom behaviors.
add	The id to add to the BiocSet object.

Value

For map_unique, a BiocSet object with unique elements.

For map_multiple, a BiocSet object with multiple mappings for certain elements.

For map_add_element, a BiocSet object with a new column in the element tibble with the mapping of the new id type.

Examples

library(org.Hs.eg.db)
es <- BiocSet(set1 = c("C5", "GANC"), set2 = c("AFM", "CGB1", "ADAM32"))
map_unique(es, org.Hs.eg.db, "SYMBOL", "ENTREZID")

map_multiple(es, org.Hs.eg.db, "SYMBOL", "ENSEMBLTRANS", "asNA")

map <- map_add_element(es, org.Hs.eg.db, "SYMBOL", "ENTREZID")
es %>% mutate_element(entrez = map)

---

Functions for mapping sets in the set tibble to different id types

Description

Functions for creating BiocSet objects from GO sets and KEGG sets, and creating a new set mapping from a current BiocSet object. map_add_set will add the mapping as a new column instead of overwriting the current one used for the mapping.

Usage

go_sets(org, from, go = c("GO", "GOID"), evidence = NULL, ontology = NULL)

kegg_sets(species)

map_set(.data, from, to)

map_add_set(.data, org, from, add)

Arguments

org	The AnnotationDbi object to identify keys/mappings from.
from	A character to indicate which identifier to map from.
go	A character to indicate the column name for the GO ids. Default is "GO".
evidence	A character to indicate the evidence codes for GO associations with a gene of interest. Default is all possible evidence codes.
ontology	A character to indicate which Gene Ontology to use. Default is BP, CC, and MF.
species	Which species the pathways are from.
.data	The BiocSet object that contains the set tibble being mapped.
to	A character to indicate which identifier to map to.
add	The id to add to the BiocSet object.

Value

For go_sets, a BiocSet object with GO ids as the set ids.

For kegg_sets, a BiocSet object with Entrez IDs reported as elements (default from KEGGREST) and KEGG pathways as sets.

For map_set, a BiocSet object with the mapped set present in the set tibble.

For map_add_set, a BiocSet object with a new column in the set tibble with the mapping of the new id type.

Examples

library(org.Hs.eg.db)
go <- go_sets(org.Hs.eg.db, "ENSEMBL")

kegg_sets("hsa")

es <- BiocSet(set1 = letters, set2 = LETTERS)
es %>% map_set("set1", "foo") 

library(GO.db)
map <- map_add_set(go, GO.db, "GOID", "DEFINITION")
go %>% mutate_set(definition = map)

---

Functions to display relationships of an OBOSet object

Description

These functions will display the relationships (children, parents, or ancestors) for either the elements or the sets of an OBOSet object.

Usage

oboset_element_children(oboset)

oboset_element_parents(oboset)

oboset_element_ancestors(oboset)

oboset_set_children(oboset)

oboset_set_parents(oboset)

oboset_set_ancestors(oboset)

Arguments

oboset

The OBOSet of interest.

Value

A 2 column tibble.

Examples

oboFile <- system.file("extdata", "sample_go.obo", package = "BiocSet")
obo <- import(oboFile)
oboset_element_children(obo) 

oboset_element_parents(obo)

oboset_element_ancestors(obo)

oboset_set_children(obo)

oboset_set_parents(obo)

oboset_set_ancestors(obo)

---

OBOSet class

Description

A class representing the 'OBO' file format as a BiocSet.

Usage

OBOSet(elementset, element, set, metadata)

Arguments

elementset	A tibble with element set information.
element	A tibble with element information.
set	A tibble with set information.
metadata	A tibble with key-value pairs describing OBO file format header data

Value

An S4 OBOOSet object. OBO sets conform to the 'obo' file format, with OBO 'Term' entries corresponding to elements. Parent / child relationships (e.g., 'is_a') are summarized as 'parents', 'ancestors', and 'children' character list columns of 'set'.

Examples

OBOSet()
oboFile <- system.file(package = "BiocSet", "extdata", "sample_go.obo")
import(oboFile)

---

Functions applied to sets in a BiocSet object

Description

All of the major methods applied to a BiocSet object can be explicitly applied to the set tibble. These functions bypass the need to use the es_activate function by indicating what function should be used on the element tibble.

Usage

filter_set(.data, ...)

select_set(.data, ...)

mutate_set(.data, ...)

summarise_set(.data, ...)

arrange_set(.data, ...)

left_join_set(.data, ...)

tibble_from_set(.data, how = unlist)

data.frame_from_set(.data, how = unlist)

Arguments

.data	A BiocSet object.
...	Additional argument passed to the function.
how	Multiple entries will become a list.

Value

A BiocSet object.

For tibble_from_set, a tibble.

For data.frame_from_set, a data.frame.

Examples

es <- BiocSet(set1 = letters, set2 = LETTERS)
filter_set(es, set == "set1")

es %>% select_set(set)

es %>% mutate_set(pval = rnorm(1:2))

es %>% summarise_set(n = n())

es %>% arrange_set(desc(set))

tbl <- tibble(x = 10:11, y = c("set1", "set2"))
es <- BiocSet(set1 = letters[c(1,3,5)], set2 = letters[c(2,4)])
left_join_set(es, tbl, by = c(set = "y"))

tibble_from_set(es)

data.frame_from_set(es)

---

Union on a single BiocSet object

Description

This function performs a union within a single BiocSet object.

Usage

union_single(x, ...)

Arguments

x	A BiocSet object.
...	Additional arguments passed to function.

Value

For union_single, a BiocSet object with a single set union and unioned elements from x.

Examples

es3 <- BiocSet(set1 = letters[c(1:10)], set2 = letters[c(4:20)])
union_single(es3)

---

Functions to access reference urls for different identifiers

Description

Functions to access reference urls for different identifiers

Usage

url_ref_element(es)

url_ref_set(es)

url_ref(es)

Arguments

es	A BiocSet object that the reference urls should be added to.

Value

For url_ref_element, a BiocSet object with the url column added to the element tibble.

For url_ref_set, a BiocSet object with the url column added to the set tibble.

For url_ref, a BiocSet object with the url column added to both the element and set tibbles.

Examples

es <- BiocSet("GO:0000002" = c("TP53", "TNF"), "GO:0000003" = c("IL6"))
url_ref_element(es) 

url_ref_set(es)

url_ref(es)

---