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Last data update: 2014.03.03

R: Parameter initialization function

pp.init

R Documentation

Parameter initialization function

Description

Parameter initialization function for pushCross and pullCross

Usage

pp.init(seg.thresh = 0.05, seg.ratio = NULL, miss.thresh = 0.1, max.rf =
        0.25, min.lod = 3)

Arguments

`seg.thresh`	Numerical value between zero and one determining the p-value threshold for the test of marker segregation distortion.
`seg.ratio`	A character string of the form "AA:BB" or "AA:AB:BB" describing the ratio of the alleles.
`miss.thresh`	Numerical value between zero and one determining the proportion of missing values.
`max.rf`	The maximum recombination fraction to consider when attempting to cluster pushed markers back into linkage groups.
`min.lod`	The minimum LOD score to consider when attempting to cluster pushed markers back into linkage groups.

Details

This parameter initialization function is used by the function pullCross to pull markers from a linkage map and pushCross to push markers back into a linkage map. How the arguments seg.thresh, seg.ratio and miss.thresh are used depends on which function is called. See pushCross and pullCross for more details.

Value

Return user defined parameter values for each of the parameters.

Author(s)

Julian Taylor

Examples


data(mapDH, package = "ASMap")

## pull markers from a linkage map with a segregation distortion

pars <- pp.init(seg.thresh = 0.05)
mapDH.s <- pullCross(mapDH, type = "seg.distortion", pars = pars)
mapDH.s$seg.distortion$table

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ASMap)
Loading required package: qtl
Loading required package: gtools
Loading required package: fields
Loading required package: spam
Loading required package: grid
Spam version 1.3-0 (2015-10-24) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

The following objects are masked from 'package:base':

    backsolve, forwardsolve

Loading required package: maps

 # maps v3.1: updated 'world': all lakes moved to separate new #
 # 'lakes' database. Type '?world' or 'news(package="maps")'.  #


Loading required package: RColorBrewer
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/ASMap/pp.init.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pp.init
> ### Title: Parameter initialization function
> ### Aliases: pp.init
> ### Keywords: misc
> 
> ### ** Examples
> 
> 
> data(mapDH, package = "ASMap")
> 
> ## pull markers from a linkage map with a segregation distortion
> 
> pars <- pp.init(seg.thresh = 0.05)
> mapDH.s <- pullCross(mapDH, type = "seg.distortion", pars = pars)
> mapDH.s$seg.distortion$table
      mark chr         pos neglog10P     missing        AA        AB
1  1A.m.26  1A  68.4700927  1.375015 0.000000000 0.5688073 0.4311927
2  1A.m.27  1A  70.3026255  1.375015 0.000000000 0.5688073 0.4311927
3  1A.m.29  1A  73.9768038  1.671789 0.000000000 0.5779817 0.4220183
4  1A.m.30  1A  75.8125081  1.375015 0.000000000 0.5688073 0.4311927
5  1A.m.32  1A  76.4333654  1.519835 0.000000000 0.5733945 0.4266055
6  1A.m.33  1A  76.8921092  1.671789 0.000000000 0.5779817 0.4220183
7  1A.m.34  1A  77.3500443  1.830929 0.000000000 0.5825688 0.4174312
8  1A.m.35  1A  85.1907512  1.375015 0.000000000 0.5688073 0.4311927
9  1A.m.36  1A  89.7685841  1.375015 0.000000000 0.5688073 0.4311927
10 1A.m.37  1A  91.1441558  1.830929 0.000000000 0.5825688 0.4174312
11 1A.m.38  1A  98.0699737  1.671789 0.000000000 0.5779817 0.4220183
12 1A.m.39  1A 100.3648637  1.519835 0.000000000 0.5733945 0.4266055
13 1A.m.40  1A 100.8234047  1.671789 0.000000000 0.5779817 0.4220183
14 1A.m.41  1A 101.2722224  1.519835 0.000000000 0.5733945 0.4266055
15  2A.m.1  2A   0.0000000  1.375015 0.000000000 0.5688073 0.4311927
16  2A.m.9  2A  51.3456384  1.671789 0.000000000 0.5779817 0.4220183
17 2A.m.29  2A 104.8080733  1.338322 0.032110092 0.5687204 0.4312796
18 2D2.m.1 2D2   0.0000000  1.519835 0.000000000 0.5733945 0.4266055
19 2D2.m.2 2D2   0.4488151  1.375015 0.000000000 0.5688073 0.4311927
20 2D2.m.3 2D2   0.9317667  1.600692 0.004587156 0.5760369 0.4239631
21 3A.m.16  3A  64.3531474  1.375015 0.000000000 0.5688073 0.4311927
22 3A.m.17  3A  64.8121744  1.451708 0.004587156 0.5714286 0.4285714
23 3A.m.19  3A  79.4373752  1.375015 0.000000000 0.5688073 0.4311927
24 3B.m.15  3B  64.1925357  1.997307 0.000000000 0.5871560 0.4128440
25 3B.m.16  3B  64.6508816  2.170970 0.000000000 0.5917431 0.4082569
26 3B.m.17  3B  65.1096201  1.872327 0.027522936 0.5849057 0.4150943
27 3B.m.18  3B  65.1096202  1.997307 0.000000000 0.5871560 0.4128440
28 3B.m.19  3B  65.5683123  1.830929 0.000000000 0.5825688 0.4174312
29 3B.m.20  3B  66.4854592  1.830929 0.000000000 0.5825688 0.4174312
30 3B.m.23  3B  79.3776517  1.600692 0.004587156 0.5760369 0.4239631
31  4B.m.1  4B   0.0000000  1.600692 0.004587156 0.5760369 0.4239631
32  4B.m.2  4B  17.7567993  1.519835 0.000000000 0.5733945 0.4266055
33  4B.m.5  4B  28.3629008  1.671789 0.000000000 0.5779817 0.4220183
34  4B.m.6  4B  31.1069464  1.375015 0.000000000 0.5688073 0.4311927
35 5B.m.31  5B 104.6713214  1.375015 0.000000000 0.5688073 0.4311927
36 5B.m.32  5B 105.5889034  1.375015 0.000000000 0.5688073 0.4311927
37 5B.m.33  5B 106.0475396  1.519835 0.000000000 0.5733945 0.4266055
38 5B.m.35  5B 107.4238503  1.375015 0.000000000 0.5688073 0.4311927
39 6D.m.12  6D  60.6944586  1.756872 0.004587156 0.4193548 0.5806452
40  7B.m.6  7B  23.0304066  1.769873 0.013761468 0.4186047 0.5813953
41  7B.m.7  7B  23.2002891  1.309862 0.004587156 0.4331797 0.5668203
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>