Description Usage Arguments Details Value Author(s) See Also Examples
Pull high LOD values with chr and pos.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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, ...)
|
scans |
object of class |
lod.thr |
LOD threshold |
drop.lod |
LOD drop from max to keep for support intervals |
extend |
extend support interval just past |
restrict.lod |
restrict to loci above LOD threshold if
|
chr |
chromosome identifier |
pos |
position, or range of positions, in cM |
x,object |
object of class |
probs |
probability levels for quantiles (should be > 0.5) |
n.quant |
maximum of |
n.pheno |
number of phenotypes considered |
max.quantile |
return only quantiles of max LOD across genome if
|
window |
size of window for smoothing hotspot size |
quant.level |
vector of LOD levels for 1 up to
|
sliding |
plot as sliding hotspot if |
... |
arguments passed along |
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.
Data frame with
row |
row number in |
phenos |
phenotype column number |
lod |
LOD score for phenotype at locus indicated by |
Brian S Yandell and Elias Chaibub Neto
1 2 3 4 5 6 | 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))
|
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