highlod function

Pull high LOD values with chr and pos.

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

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)
• chr: chromosome identifier
• pos: position, or range of positions, in cM
• x,object: object of class highlod
• probs: probability levels for quantiles (should be > 0.5)
• n.quant: maximum of s.quant
• n.pheno: number of phenotypes considered
• max.quantile: return only quantiles of max LOD across genome if TRUE
• window: size of window for smoothing hotspot size
• quant.level: vector of LOD levels for 1 up to length(quant.level) size hotspots
• sliding: plot as sliding hotspot if TRUE
• ...: arguments passed along

See Also

highlod, hotperm

Returns

Data frame with - row: row number in scanone object

• phenos: phenotype column number

• lod: LOD score for phenotype at locus indicated by row

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.

Author(s)

Brian S Yandell and Elias Chaibub Neto

Examples

example(include.hotspots)
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))