RangedTupleList methods

Container and metadata methods shared by every RangedTupleList subclass.

nrow() counts elements, ncol() counts metadata columns and colnames() names them, so the collections read exactly as the DFrame-shaped ones they replace. $ and $<- read and write mcols columns. [ selects elements and rejects a second argument, because the stock method would silently discard it. endoapply() maps over the elements and rebuilds the object with its collection-level slots intact.

Usage

# S4 method for class 'RangedTupleList'
nrow(x)

# S4 method for class 'RangedTupleList'
ncol(x)

# S4 method for class 'RangedTupleList'
colnames(x, do.NULL = TRUE, prefix = "col")

# S4 method for class 'RangedTupleList'
x$name

# S4 method for class 'RangedTupleList'
x$name <- value

# S4 method for class 'RangedTupleList,ANY,ANY,ANY'
x[i, j, ..., drop = TRUE]

# S4 method for class 'RangedTupleList,ANY,ANY'
x[[i, j, ...]] <- value

# S4 method for class 'RangedTupleList'
endoapply(X, FUN, ...)

# S4 method for class 'RangedTupleList'
bindROWS(
  x,
  objects = list(),
  use.names = TRUE,
  ignore.mcols = FALSE,
  check = TRUE
)

Arguments

x, X

A RangedTupleList collection.

do.NULL, prefix

Unused; present for generic compatibility.

name

An mcols column name.

value

Replacement value for that column.

i

Element selector.

j

Not supported; supplying it is an error.

...

Additional arguments passed on.

drop

Passed through to the inherited method.

FUN

A function applied to each element, returning a GRanges.

Value

nrow() and ncol() integers; colnames() a character vector; $ a metadata column; $<-, [ and endoapply() a collection of the same class.

Examples

data(qtlSumStatsMulticontextExample)
mc <- qtlSumStatsMulticontextExample
# A collection reads as a table of tuples: one row per element, with the
# identity in mcols and the variants in the element itself.
nrow(mc)
#> [1] 3
ncol(mc)
#> [1] 4
colnames(mc)
#> [1] "study"   "context" "trait"   "varY"   
mc$context
#> [1] "brain"  "blood"  "muscle"
length(mc[[1]])
#> [1] 200
# Row subsetting and endoapply() both return the same class, carrying the
# collection-level slots with them.
class(mc[1:2])
#> [1] "QtlSumStats"
#> attr(,"package")
#> [1] "pecotmr"
lengths(endoapply(mc, head, n = 5L))
#> [1] 5 5 5