find_marker {qtl2}

Find markers by chromosome position

Description

Find markers closest to specified set of positions, or within a specified interval.

Usage

find_marker(map, chr, pos = NULL, interval = NULL)

Arguments

map

A map object: a list (corresponding to chromosomes) of vectors of marker positions. Can also be a snpinfo object (data frame with columns chr and pos; marker names taken from column snp or if that doesn't exist from the row names)

chr

A vector of chromosomes

pos

A vector of positions

interval

A pair of positions (provide either pos or interval but not both)

Details

If pos is provided, interval should not be, and vice versa.

If pos is provided, then chr and pos should either be the same length, or one of them should have length 1 (to be expanded to the length of the other).

If interval is provided, then chr should have length 1.

Value

A vector of marker names, either closest to the positions specified by pos, or within the interval defined by interval.

See Also

find_markerpos(), find_index_snp(), pull_genoprobpos(), pull_genoprobint()

Examples

iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))

# find markers by their genetic map positions
find_marker(iron$gmap, c(8, 11), c(37.7, 56.9))

# find markers by their physical map positions (two markers on chr 7)
find_marker(iron$pmap, 7, c(44.2, 108.9))

# find markers in an interval
find_marker(iron$pmap, 16, interval=c(35, 80))