IndexedFst-class: IndexedFst

In ETHZ-INS/scanMiRApp: scanMiR shiny application

IndexedFst

Description

Objects of the IndexedFst class enable fast named random access to FST files. This is particularly appropriate for large data.frames which often need to be accessed according to the (e.g. factor) value of a particular column.

Usage

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

## S4 method for signature 'IndexedFst'
summary(object)

## S4 method for signature 'IndexedFst'
names(x)

## S4 method for signature 'IndexedFst'
length(x)

## S4 method for signature 'IndexedFst'
lengths(x)

## S4 method for signature 'IndexedFst'
nrow(x)

## S4 method for signature 'IndexedFst'
ncol(x)

## S4 method for signature 'IndexedFst'
colnames(x)

## S4 method for signature 'IndexedFst,ANY,ANY'
x[[i, j = NULL, ...]]

## S4 method for signature 'IndexedFst,ANY,ANY,ANY'
x[i, j = NULL, ..., drop = TRUE]

## S4 method for signature 'IndexedFst'
x$name

## S4 method for signature 'IndexedFst'
head(x, n = 6L, ...)

## S4 method for signature 'IndexedFst'
as.data.frame(x, name)

Arguments

object	an IndexedFst object
x	an IndexedFst object
i	the desired index (either numeric or name)
j, drop	ignored
...	ignored
name	the indexed name to fetch
n	the desired number of rows

Value

Depends on the method

Author(s)

Pierre-Luc Germain, [e-mail]

See Also

saveIndexedFst, loadIndexedFst

Examples

# we first create and save an indexed FST file
tmp <- tempdir()
f <- system.file(tmp, "test")
d <- data.frame( category=sample(LETTERS[1:4], 10000, replace=TRUE),
                 var2=sample(LETTERS, 10000, replace=TRUE),
                 var3=runif(10000) )
format(object.size(d),units="Kb")
saveIndexedFst(d, "category", f)
rm(d)
# we then load the index, and can use category names for random access:
d <- loadIndexedFst(f)
format(object.size(d),units="Kb")
nrow(d)
names(d)
head(d$A)

ETHZ-INS/scanMiRApp documentation built on March 16, 2024, 5:30 p.m.