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Last data update: 2014.03.03

R: Pull markers from a linkage map.

pullCross

R Documentation

Pull markers from a linkage map.

Description

Pull markers of a certain type from a linkage map and place them aside in the R/qtl object and, if appropriate, keeping their connections with the reduced linkage map.

Usage

pullCross(object, chr, type = c("co.located","seg.distortion","missing"),
          pars = NULL, replace = FALSE, ...)

Arguments

`object`	An R/qtl `cross` object with class structure `"bc", "dh","riself","bcsft"`. (see `?mstmap.cross` for more details.)
`chr`	A character vector of linkage group names with which to subset the linkage map before pulling any markers.
`type`	A character string determining the type of markers to be pulled from the map (see Details).
`pars`	A list of parameters that are used by `pullCross` to pull markers of certain type. The default NULL calls the parameter initialization function `pp.init` with defaults (see Details and Examples).
`replace`	A logical value determining whether the markers and summary of marker information that is pulled from the map replaces information that is already residing in the `type` element of the object.
`...`	Currently ignored.

Details

This function gives users the ability to "pull" markers of several different types from the linkage map and place them in appropriately named elements of the cross object. These elements can be examined by the user and can even be "pushed" back using the complementary command pushCross.

Currently supported types are:

type = "co.located". This type gives the user the ability to reduce a linkage map to a unique set of markers for the purpose of efficient map construction. Co-located markers are pulled from the linkage map using the technology of findDupMarkers from the qtl package and places them aside in a separate list element called "co.located". This element contains the removed marker data as well as a table that displays the connections between the co-located markers with markers that remain in the linkage map. If required, this table is used by pushCross to "push" the co-located markers back into the linkage map.
type = "seg.distortion". Users can pull markers with segregation distortion from a linkage map with two different thresholding mechanisms called using pars. If the list argument pars is used with an element called seg.thresh then markers are pulled from the map if the p-value from the test for segregation distortion is LESS than seg.thresh. Values of seg.thresh must be between 0 and 1. If pars contains an element seg.ratio then markers are pulled from the map based on the ratio provided. The ratio must be in character format and of the type "AA:BB" for two allele populations and "AA:AB:BB" for three allele populations (see Examples for more details). Markers are pulled if their allele proportions are GREATER than the largest proportional ratio or LESS than the smallest proportional ratio given in seg.thresh. If neither thresholding mechanisms are given then the default is to use seg.thresh = 0.05. If markers are found matching the above criteria they are pulled from the linkage map and placed aside in an element called "seg.distortion". This element contains the removed distorted marker data as well as a table summarizing each of the markers. See examples below for more detail.
type = "missing". Users can pull markers with a proportional amount of missing allele scores. If pars contains an element miss.thresh then markers are pulled from the linkage map that have a proportion of missing values GREATER than miss.thresh. If no value is given for miss.thresh then it defaults to 0.1 or 10% missing values. If markers are found matching the above criteria they are pulled from the map and are placed aside in an separate list element called "missing". This element contains the removed marker data as well as a table summarizing each of the markers. See examples below for more detail.

Value

The cross object is returned with identical class structure as the inputted cross object and an additional elements corresponding to the marker types being pulled from the map.

Author(s)

Julian Taylor

Examples


data(mapDH, package = "ASMap")

## pull co-located markers from linkage map

mapDH.c <- pullCross(mapDH, type = "co.located")
mapDH.c$co.located$table

## pull distorted markers from linkage map using seg.thresh

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

## pull distorted markers from linkage map using seg.ratio

mapDH.s <- pullCross(mapDH, type = "seg.distortion", pars =
            list(seg.ratio = "56:44"))
mapDH.s$seg.distortion$table

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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/pullCross.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pullCross
> ### Title: Pull markers from a linkage map.
> ### Aliases: pullCross
> ### Keywords: misc
> 
> ### ** Examples
> 
> 
> data(mapDH, package = "ASMap")
> 
> ## pull co-located markers from linkage map
> 
> mapDH.c <- pullCross(mapDH, type = "co.located")
> mapDH.c$co.located$table
   bins chr    mark
1     1 1B1 1B1.m.4
2     1 1B1 1B1.m.5
3     2  1D  1D.m.3
4     2  1D  1D.m.4
5     3  2B 2B.m.31
6     3  2B 2B.m.32
7     4 2D1 2D1.m.6
8     4 2D1 2D1.m.7
9     5  3A 3A.m.35
10    5  3A 3A.m.36
11    6  3B 3B.m.11
12    6  3B 3B.m.12
13    7  3D  3D.m.1
14    7  3D  3D.m.2
15    8  4A  4A.m.7
16    8  4A  4A.m.8
17    9  5A 5A.m.36
18    9  5A 5A.m.37
19   10  5B 5B.m.15
20   10  5B 5B.m.16
21   11  5D  5D.m.4
22   11  5D  5D.m.5
23   12  6D  6D.m.2
24   12  6D  6D.m.3
25   13  7A 7A.m.32
26   13  7A 7A.m.33
27   14  7B 7B.m.21
28   14  7B 7B.m.22
29   15  7D  7D.m.2
30   15  7D  7D.m.3
> 
> ## pull distorted markers from linkage map using seg.thresh
> 
> mapDH.s <- pullCross(mapDH, type = "seg.distortion", pars =
+            list(seg.thresh = 0.05))
> 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
> 
> ## pull distorted markers from linkage map using seg.ratio
> 
> mapDH.s <- pullCross(mapDH, type = "seg.distortion", pars =
+             list(seg.ratio = "56:44"))
> 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.28  1A  70.7609297  1.237267 0.000000000 0.5642202 0.4357798
4  1A.m.29  1A  73.9768038  1.671789 0.000000000 0.5779817 0.4220183
5  1A.m.30  1A  75.8125081  1.375015 0.000000000 0.5688073 0.4311927
6  1A.m.32  1A  76.4333654  1.519835 0.000000000 0.5733945 0.4266055
7  1A.m.33  1A  76.8921092  1.671789 0.000000000 0.5779817 0.4220183
8  1A.m.34  1A  77.3500443  1.830929 0.000000000 0.5825688 0.4174312
9  1A.m.35  1A  85.1907512  1.375015 0.000000000 0.5688073 0.4311927
10 1A.m.36  1A  89.7685841  1.375015 0.000000000 0.5688073 0.4311927
11 1A.m.37  1A  91.1441558  1.830929 0.000000000 0.5825688 0.4174312
12 1A.m.38  1A  98.0699737  1.671789 0.000000000 0.5779817 0.4220183
13 1A.m.39  1A 100.3648637  1.519835 0.000000000 0.5733945 0.4266055
14 1A.m.40  1A 100.8234047  1.671789 0.000000000 0.5779817 0.4220183
15 1A.m.41  1A 101.2722224  1.519835 0.000000000 0.5733945 0.4266055
16  2A.m.1  2A   0.0000000  1.375015 0.000000000 0.5688073 0.4311927
17  2A.m.9  2A  51.3456384  1.671789 0.000000000 0.5779817 0.4220183
18 2A.m.20  2A  88.6135963  1.237267 0.000000000 0.5642202 0.4357798
19 2A.m.26  2A 101.5237715  1.121967 0.018348624 0.5607477 0.4392523
20 2A.m.29  2A 104.8080733  1.338322 0.032110092 0.5687204 0.4312796
21 2D2.m.1 2D2   0.0000000  1.519835 0.000000000 0.5733945 0.4266055
22 2D2.m.2 2D2   0.4488151  1.375015 0.000000000 0.5688073 0.4311927
23 2D2.m.3 2D2   0.9317667  1.600692 0.004587156 0.5760369 0.4239631
24 3A.m.16  3A  64.3531474  1.375015 0.000000000 0.5688073 0.4311927
25 3A.m.17  3A  64.8121744  1.451708 0.004587156 0.5714286 0.4285714
26 3A.m.18  3A  64.8121745  1.237267 0.000000000 0.5642202 0.4357798
27 3A.m.19  3A  79.4373752  1.375015 0.000000000 0.5688073 0.4311927
28 3A.m.20  3A  82.6518066  1.237267 0.000000000 0.5642202 0.4357798
29 3A.m.22  3A  83.7972184  1.237267 0.000000000 0.5642202 0.4357798
30 3B.m.15  3B  64.1925357  1.997307 0.000000000 0.5871560 0.4128440
31 3B.m.16  3B  64.6508816  2.170970 0.000000000 0.5917431 0.4082569
32 3B.m.17  3B  65.1096201  1.872327 0.027522936 0.5849057 0.4150943
33 3B.m.18  3B  65.1096202  1.997307 0.000000000 0.5871560 0.4128440
34 3B.m.19  3B  65.5683123  1.830929 0.000000000 0.5825688 0.4174312
35 3B.m.20  3B  66.4854592  1.830929 0.000000000 0.5825688 0.4174312
36 3B.m.23  3B  79.3776517  1.600692 0.004587156 0.5760369 0.4239631
37 3B.m.25  3B  98.0628133  1.237267 0.000000000 0.5642202 0.4357798
38  4B.m.1  4B   0.0000000  1.600692 0.004587156 0.5760369 0.4239631
39  4B.m.2  4B  17.7567993  1.519835 0.000000000 0.5733945 0.4266055
40  4B.m.3  4B  18.2134551  1.121967 0.018348624 0.5607477 0.4392523
41  4B.m.5  4B  28.3629008  1.671789 0.000000000 0.5779817 0.4220183
42  4B.m.6  4B  31.1069464  1.375015 0.000000000 0.5688073 0.4311927
43  5A.m.3  5A   6.9074284  1.237267 0.000000000 0.4357798 0.5642202
44 5A.m.25  5A 102.1256749  1.237267 0.000000000 0.4357798 0.5642202
45 5B.m.31  5B 104.6713214  1.375015 0.000000000 0.5688073 0.4311927
46 5B.m.32  5B 105.5889034  1.375015 0.000000000 0.5688073 0.4311927
47 5B.m.33  5B 106.0475396  1.519835 0.000000000 0.5733945 0.4266055
48 5B.m.34  5B 106.9651677  1.237267 0.000000000 0.5642202 0.4357798
49 5B.m.35  5B 107.4238503  1.375015 0.000000000 0.5688073 0.4311927
50 5B.m.36  5B 107.8823913  1.237267 0.000000000 0.5642202 0.4357798
51 5B.m.37  5B 110.1780101  1.175090 0.004587156 0.5622120 0.4377880
52 5B.m.41  5B 112.4717114  1.237267 0.000000000 0.5642202 0.4357798
53 5B.m.53  5B 121.6485891  1.237267 0.000000000 0.5642202 0.4357798
54 6B.m.12  6B  45.1327419  1.237267 0.000000000 0.5642202 0.4357798
55 6D.m.12  6D  60.6944586  1.756872 0.004587156 0.4193548 0.5806452
56  7B.m.6  7B  23.0304066  1.769873 0.013761468 0.4186047 0.5813953
57  7B.m.7  7B  23.2002891  1.309862 0.004587156 0.4331797 0.5668203
58 7B.m.19  7B  33.5252305  1.237267 0.000000000 0.4357798 0.5642202
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>