BiocSet-methods {BiocSet} | R Documentation |
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 NA
s 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.
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, ...)
.data |
The |
what |
Which of the three tibbles from |
... |
Additional arguments passed to function. |
x |
For |
add |
logical, whether to add to the existing groups. |
y |
For |
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. |
A BiocSet
object.
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)