hotsize: Hotspot size routines.

Description Usage Arguments Value Author(s) See Also Examples

Description

Determine hotspot sizes and display. Use individual threshold and quantile thresholds as provided.

Usage

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hotsize(hotobject, ...)
## S3 method for class 'scanone'
hotsize(hotobject, lod.thr = NULL, drop.lod = 1.5, ...)
## S3 method for class 'highlod'
hotsize(hotobject, lod.thr = NULL, window = NULL,
  quant.level = NULL, ...)
## S3 method for class 'hotsize'
print(x, ...)
## S3 method for class 'hotsize'
summary(object, ...)
## S3 method for class 'hotsize'
plot(x, ylab = "counts", quant.axis = pretty(x$max.N),
  col = c("black", "red", "blue"), by.chr = FALSE, maps = NULL,
  title = "",...)

Arguments

hotobject

object of class scanone or highlod

lod.thr

LOD threshold

drop.lod

LOD drop from max to keep for support intervals

window

window width in cM for smoothing hotspot size; not used if 0 or NULL

quant.level

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

x,object

object of class hotsize

ylab

label for vertical plot axis

quant.axis

hotspot sizes for quantile axis (vertical on right side of plot)

col

col of hotspot size, smoothed hotspot size, and sliding hotspot size

by.chr

separate plot by chromosome if TRUE

maps

if not NULL, list of objects of class map to use for rugs on top and bottom of plot

title

title for plot

...

arguments passed along to scanone methods

Value

hotsize methods return an object of class hotsize, which is essentially an object of class summary.scanone with additional attributes for lod.thr, window, and quant.level.

Author(s)

Brian S Yandell and Elias Chaibub Neto

See Also

highlod, hotperm

Examples

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example(highlod)
hots1 <- hotsize(high1)
summary(hots1)
plot(hots1)

Example output

Loading required package: qtl
Loading required package: lattice
Loading required package: corpcor
Loading required package: mnormt

highld> example(include.hotspots)

incld.> ncross1 <- sim.null.cross(chr.len = rep(100, 4),
incld.+                           n.mar = 51,
incld.+                           n.ind = 100,
incld.+                           type = "bc",
incld.+                           n.phe = 1000,
incld.+                           latent.eff = 3,
incld.+                           res.var = 1,
incld.+                           init.seed = 123457)

incld.> cross1 <- include.hotspots(cross = ncross1,
incld.+                            hchr = c(2, 3, 4),
incld.+                            hpos = c(25, 75, 50),
incld.+                            hsize = c(100, 50, 20),
incld.+                            Q.eff = 2,
incld.+                            latent.eff = 3,
incld.+                            lod.range.1 = c(2.5, 2.5),
incld.+                            lod.range.2 = c(5, 8),
incld.+                            lod.range.3 = c(10, 15),
incld.+                            res.var = 1,
incld.+                            n.phe = 1000,
incld.+                            init.seed = 12345)

highld> scan1 <- scanone(cross1, pheno.col = 1:1000, method = "hk")

highld> high1 <- highlod(scan1, lod.thr = 2.11, drop.lod = 1.5)

highld> pull.highlod(high1, chr = 2, pos = 24)
         chr pos phenos      lod
D2M13      2  24     P2 3.388776
D2M13.1    2  24     P6 3.002020
D2M13.2    2  24     P8 3.430235
D2M13.3    2  24    P18 2.272088
D2M13.4    2  24    P35 2.877761
D2M13.5    2  24    P42 2.627779
D2M13.6    2  24    P45 3.314888
D2M13.7    2  24    P53 3.598085
D2M13.8    2  24    P56 2.460279
D2M13.9    2  24    P58 3.439272
D2M13.10   2  24    P72 3.849090
D2M13.11   2  24    P76 3.381574
D2M13.12   2  24    P87 2.838147
D2M13.13   2  24   P129 2.437061
D2M13.14   2  24   P133 2.792576
D2M13.15   2  24   P139 3.018036
D2M13.16   2  24   P140 2.984040
D2M13.17   2  24   P151 3.040573
D2M13.18   2  24   P166 3.823492
D2M13.19   2  24   P176 2.982420
D2M13.20   2  24   P182 4.150266
D2M13.21   2  24   P202 2.837522
D2M13.22   2  24   P205 2.759836
D2M13.23   2  24   P221 3.514802
D2M13.24   2  24   P223 2.727625
D2M13.25   2  24   P243 3.954829
D2M13.26   2  24   P249 2.750183
D2M13.27   2  24   P280 2.855761
D2M13.28   2  24   P299 3.022717
D2M13.29   2  24   P307 2.971370
D2M13.30   2  24   P312 3.200077
D2M13.31   2  24   P320 2.735781
D2M13.32   2  24   P324 3.263333
D2M13.33   2  24   P347 4.481063
D2M13.34   2  24   P349 3.540741
D2M13.35   2  24   P358 2.915029
D2M13.36   2  24   P359 3.256071
D2M13.37   2  24   P381 3.334650
D2M13.38   2  24   P382 2.636571
D2M13.39   2  24   P386 3.208191
D2M13.40   2  24   P396 2.907832
D2M13.41   2  24   P411 2.760250
D2M13.42   2  24   P412 3.040671
D2M13.43   2  24   P445 2.831598
D2M13.44   2  24   P455 2.815784
D2M13.45   2  24   P456 3.251606
D2M13.46   2  24   P459 3.470346
D2M13.47   2  24   P466 3.444492
D2M13.48   2  24   P470 2.118428
D2M13.49   2  24   P471 2.736852
D2M13.50   2  24   P472 3.314180
D2M13.51   2  24   P473 3.929050
D2M13.52   2  24   P506 3.310885
D2M13.53   2  24   P530 2.944440
D2M13.54   2  24   P546 3.648390
D2M13.55   2  24   P560 3.597727
D2M13.56   2  24   P573 2.796950
D2M13.57   2  24   P594 4.496695
D2M13.58   2  24   P595 2.981309
D2M13.59   2  24   P605 2.462974
D2M13.60   2  24   P630 3.754764
D2M13.61   2  24   P641 3.734657
D2M13.62   2  24   P648 3.321849
D2M13.63   2  24   P651 2.929950
D2M13.64   2  24   P660 3.430068
D2M13.65   2  24   P678 2.899678
D2M13.66   2  24   P681 2.963974
D2M13.67   2  24   P689 3.699696
D2M13.68   2  24   P692 2.831405
D2M13.69   2  24   P693 3.059182
D2M13.70   2  24   P710 2.972535
D2M13.71   2  24   P721 2.437751
D2M13.72   2  24   P722 2.816196
D2M13.73   2  24   P727 2.641131
D2M13.74   2  24   P733 3.236445
D2M13.75   2  24   P735 3.395650
D2M13.76   2  24   P740 3.386157
D2M13.77   2  24   P745 4.043596
D2M13.78   2  24   P751 3.200972
D2M13.79   2  24   P755 3.137649
D2M13.80   2  24   P760 3.107310
D2M13.81   2  24   P770 3.228695
D2M13.82   2  24   P786 3.007986
D2M13.83   2  24   P801 2.829519
D2M13.84   2  24   P838 2.382058
D2M13.85   2  24   P845 2.794768
D2M13.86   2  24   P871 2.746736
D2M13.87   2  24   P875 2.782606
D2M13.88   2  24   P882 3.050230
D2M13.89   2  24   P884 2.646522
D2M13.90   2  24   P887 2.999239
D2M13.91   2  24   P889 3.605486
D2M13.92   2  24   P917 3.511876
D2M13.93   2  24   P918 3.033706
D2M13.94   2  24   P925 3.052736
D2M13.95   2  24   P934 3.630265
D2M13.96   2  24   P945 2.979431
D2M13.97   2  24   P958 3.247551
D2M13.98   2  24   P971 3.571035
D2M13.99   2  24   P981 3.555443

highld> summary(high1, lod.thr = 2.44)
hotsize elements:  chr pos max.N 
LOD threshold: 2.44 

      chr pos max.N
D1M48   1  94    41
D2M13   2  24    95
D3M36   3  70    50
D4M25   4  48    20

highld> max(high1, lod.thr = seq(2.11, 3.11, by = .1))
       chr pos max.N lod.thr
D1M34    1  66   126    2.11
D2M13    2  24    99    2.21
D2M12    2  22    98    2.31
D2M131   2  24    97    2.41
D2M132   2  24    93    2.51
D2M121   2  22    93    2.61
D2M133   2  24    89    2.71
D2M122   2  22    78    2.81
D2M123   2  22    67    2.91
D2M134   2  24    54    3.01
D3M38    3  74    50    3.11
hotsize elements:  chr pos max.N 
LOD threshold: 2.11 

      chr pos max.N
D1M34   1  66   126
D2M12   2  22   100
D3M36   3  70    50
D4M23   4  44    20

qtlhot documentation built on May 2, 2019, 11:06 a.m.