BiocSet-methods: BiocSet methods

In Kayla-Morrell/GeneSet: Representing Different Biological Sets

Description

es_activate: which of the three tibbles in the BiocSet object should be activated and have the chosen functionality applied to it.

filter: choose rows where conditions are true.

select: keep only the variables listed.

mutate: add new variable and preserve the existing variables.

summarise: usually used with group_by(), output will have one row for each group.

arrange: order rows by an expression involving its variables.

.tbl_nongroup_vars: returns only non-grouping variables.

group_by: converts an existing tbl into a grouped tbl.

left_join: returns all rows from x, and all columns from x and y. If no rows in x match with y there will be NAs in the new column. If there are multiple matches then all combinations are returned.

as.list: coerces argument into a list.

union: combines all rows from two BiocSet objects and removes duplicate records from the combined BiocSet object.

intersect: combines all rows from two BiocSet objects and returns rows that appear in both BiocSet objects.

Usage

es_activate(.data, what)

## S3 method for class 'BiocSet'
filter(.data, ...)

## S3 method for class 'BiocSet'
select(.data, ...)

## S3 method for class 'BiocSet'
mutate(.data, ...)

## S3 method for class 'BiocSet'
summarise(.data, ...)

## S3 method for class 'BiocSet'
arrange(.data, ...)

.tbl_nongroup_vars.BiocSet(x)

## S3 method for class 'BiocSet'
group_by(.data, ..., add = FALSE)

## S3 method for class 'BiocSet'
left_join(x, y, by, copy, suffix, ...)

## S3 method for class 'BiocSet'
as.list(x, ...)

## S3 method for class 'BiocSet'
union(x, y, ...)

## S3 method for class 'BiocSet'
intersect(x, y, ...)

Arguments

.data	The BiocSet object.
what	Which of the three tibbles from BiocSet to activate.
...	Additional arguments passed to function.
x	For .tbl_nongroup_vars (internal), a BiocSet object. For union and intersect the first BiocSet object to perform the operations on.
add	logical, whether to add to the existing groups.
y	For left_join, a tibble to join. For union and intersect the second BiocSet object used.
by	A character vector of variables to join by.
copy	logical, allows you to join tables across srcs.
suffix	Character vector of length 2, if there are non-joined duplicate variables in 'x' and 'y' these suffixes will be added to the output.

Value

A BiocSet object.

Examples

es <- BiocSet(set1 = letters, set2 = LETTERS)
es_activate(es, element)

es %>% es_activate(element) %>% filter(element == "a")

es %>% select(element)

es %>% es_activate(set) %>% mutate(pval = rnorm(1:2))

es %>% es_activate(set) %>% summarise(n = n())

es %>% es_activate(element) %>% arrange(desc(element))

es %>% mutate(pval = rnorm(1:52)) %>% es_elementset() %>%
    BiocSet:::.tbl_nongroup_vars()

es %>% group_by(element, set)

es <- BiocSet(set1 = letters[1:5], set2 = LETTERS[1:5])
tbl <- tibble(x = 1:10, y = c(letters[1:5], LETTERS[1:5]))
es %>% left_join(tbl, by = c(element = "y"))

library(org.Hs.eg.db)
es <- go_sets(org.Hs.eg.db, "ENSEMBL")
head(as.list(es))

es1 <- BiocSet(set1 = letters[c(1:4)], set2 = LETTERS[c(1:4)])
es2 <- BiocSet(set1 = letters[c(3:8)], set2 = LETTERS[c(3:8)])

dplyr::union(es1, es2)

dplyr::intersect(es1, es2)

Kayla-Morrell/GeneSet documentation built on April 15, 2020, 11:43 p.m.