qtlhot (version 1.2.10)

highlod: Pull high LOD values with chr and pos.

Description

Pull high LOD values with chr and pos.

Usage

highlod(
  scans,
  lod.thr = 0,
  drop.lod = 1.5,
  extend = TRUE,
  restrict.lod = FALSE,
  ...
)
# S3 method for highlod
print(x, ...)
# S3 method for highlod
summary(object, ...)
# S3 method for highlod
plot(x, ..., quant.level = NULL, sliding = FALSE)
pull.highlod(object, chr, pos, ...)
# S3 method for highlod
max(x, lod.thr = NULL, window = NULL, quant.level = NULL, ...)

Value

Data frame with

row

row number in scanone object

phenos

phenotype column number

lod

LOD score for phenotype at locus indicated by row

Arguments

scans

object of class scanone

lod.thr

LOD threshold

drop.lod

LOD drop from max to keep for support intervals

extend

extend support interval just past drop.lod; matches behavior of lodint when TRUE

restrict.lod

restrict to loci above LOD threshold if TRUE; matches behavior of lodint when FALSE (default)

...

arguments passed along

x, object

object of class highlod

quant.level

vector of LOD levels for 1 up to length(quant.level) size hotspots

sliding

plot as sliding hotspot if TRUE

chr

chromosome identifier

pos

position, or range of positions, in cM

window

size of window for smoothing hotspot size

Author

Brian S Yandell and Elias Chaibub Neto

Details

The highlod condenses a scanone object to the peaks above a lod.thr and/or within drop.lod of such peaks. The pull.highlod pulls out the entries at a particular genomic location or interval of locations. Summary, print, plot, max and quantile methods provide ways to examine a highlod object.

See Also

highlod, hotperm

Examples

ncross1 <- sim.null.cross(chr.len = rep(100, 4),
                          n.mar = 51,
                          n.ind = 100,
                          type = "bc",
                          n.phe = 1000,
                          latent.eff = 3,
                          res.var = 1,
                          init.seed = 123457)
cross1 <- include.hotspots(cross = ncross1,
                           hchr = c(2, 3, 4),
                           hpos = c(25, 75, 50),
                           hsize = c(100, 50, 20),
                           Q.eff = 2,
                           latent.eff = 3,
                           lod.range.1 = c(2.5, 2.5),
                           lod.range.2 = c(5, 8),
                           lod.range.3 = c(10, 15),
                           res.var = 1,
                           n.phe = 1000,
                           init.seed = 12345)
scan1 <- scanone(cross1, pheno.col = 1:1000, method = "hk")
high1 <- highlod(scan1, lod.thr = 2.11, drop.lod = 1.5)
pull.highlod(high1, chr = 2, pos = 24)
summary(high1, lod.thr = 2.44)
max(high1, lod.thr = seq(2.11, 3.11, by = .1))