README.md

In eriqande/inbredPermute: Simple permutation procedures for distributions of rxy values amongst parents

README

inbredPermute

Simple scripts/procedures in development to permute values of rxy around to see if survival is related to inbreeding in salmon pedigrees. Joint work with David Vendrami.

Basic workflow

The basic idea here is that we should be able to proceed directly with two ingredients:

1. A raw kingroup output file that includes $r_{xy}$ values. The top of that file should look something like this:

   *, This is the results file [in KINSHIP format] of KINGROUP v2_090501 *, Saved at 21:41 gio lug 17 2014 *, Column delimiter: comma *, Last saved file: Asus\Desktop\MKHM_kingroup_output *, Last imported file: CVB11_12_13_14\NEW\MKHM_kingroup_input.txt *, Population *, *, ALLELE FREQUENCY BLOCK

2. A list of trios that were found in the population, that include offspring whose parents are the ones that were included in the kingroup analysis. I must have three columns that are named Ma, Pa, and Kid (which are case-sensitive), and it can have any other columns that you might happen to have in there, too. Here is an example:

   Kid Pa Ma MKHM130058 MKHM100005 MKHM100004 MKHM130049 MKHM100007 MKHM100006 MKHM130045 MKHM100009 MKHM100008 MKHM130030 MKHM100016 MKHM100015 MKHM140072 MKHM100021 MKHM100020 FRHM130259 MKHM100021 MKHM100020 MKHM140026 MKHM100023 MKHM100022 FRHM130841 MKHM100027 MKHM100026 MKHM140042 MKHM100027 MKHM100026

3. A file with spawn date and sex of individuals in this sort of format:

   TK_ID Sex SpawnDate MKHM100001 Female 12/9/10 MKHM100002 Male 12/9/10 MKHM100003 Male 12/9/10 MKHM100004 Female 12/9/10 MKHM100005 Male 12/9/10 MKHM100006 Female 12/9/10 MKHM100007 Male 12/9/10 MKHM100008 Female 12/16/10 MKHM100009 Male 12/16/10

Then, to run the function you would do something like:

    library(inbredPermute)

## Loading required package: plyr

    simmat <- do_the_perms(kg_file = system.file("data_files/MKHM_kingroup_output.csv", package="inbredPermute", mustWork = T),
                           trio_file = system.file("data_files/MKHM_trios.txt", package="inbredPermute", mustWork = T),
                           meta_file = system.file("data_files/MKHM2011_metadata.txt", package="inbredPermute", mustWork = T),
                           ItalianCommas = TRUE,
                           REPS = 100  # you will want to do more in practice
                           )

    simmat[1:10, 1:10]

##                Reps
## SimmedOffspring       1       2       3       4       5       6       7
##              1  -0.0413 -0.2131 -0.3201  0.0855 -0.2790 -0.1911 -0.0233
##              2  -0.0580 -0.2512  0.0008 -0.0883 -0.0946 -0.1339  0.1077
##              3  -0.0580 -0.2512  0.0008 -0.0883 -0.0946 -0.1339  0.1077
##              4  -0.0129  0.0089 -0.1236  0.0092 -0.0233  0.0890  0.0855
##              5  -0.0129  0.0089 -0.1236  0.0092 -0.0233  0.0890  0.0855
##              6   0.1126 -0.0792  0.0358 -0.0582  0.4861  0.0695 -0.1714
##              7  -0.0666 -0.1197 -0.0139  0.0837  0.0850  0.2243 -0.0510
##              8  -0.0666 -0.1197 -0.0139  0.0837  0.0850  0.2243 -0.0510
##              9  -0.0666 -0.1197 -0.0139  0.0837  0.0850  0.2243 -0.0510
##              10 -0.1197 -0.1189 -0.1197 -0.0139 -0.0980 -0.0472 -0.2271
##                Reps
## SimmedOffspring       8       9      10
##              1  -0.1225 -0.1112 -0.1684
##              2  -0.1048 -0.0129  0.5008
##              3  -0.1048 -0.0129  0.5008
##              4  -0.0194  0.0807 -0.1225
##              5  -0.0194  0.0807 -0.1225
##              6   0.0685 -0.0644 -0.0355
##              7  -0.0326  0.1397 -0.0980
##              8  -0.0326  0.1397 -0.0980
##              9  -0.0326  0.1397 -0.0980
##              10 -0.0893  0.0487 -0.0360

Terms

As a work partially of the United States Government, this package is in the public domain within the United States.

Of course, it would be awfully lame of anyone to take anything found within here and use it as their own before we tried publishing any of this, should we choose to do that.

See TERMS.md for more information.

eriqande/inbredPermute documentation built on May 16, 2019, 8:47 a.m.