kinship pipeline

kinship specifications

Information


Unique identifier OMICS_11091
Name kinship
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.6.4
Stability Stable
Requirements Matrix, quadprog
Maintained Yes

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Documentation


Maintainer


  • person_outline Jason Sinnwell <>

Publications for kinship

kinship citations

 (13)
2018
PMCID: 5848162

[…] in the panel was done via genotyping by sequencing (gbs) according to [71]. a data subset consisting of 2000 snps was used to calculate population substructure using structure 2.2 [72], and a kinship matrix using powermarker v. 3.25 [73] to correct for population substructure during association analysis using the mixed linear model of tassel 3.0.1 [74]. snps within the reported genetic […]

2018
PMCID: 5915555

[…] participating in the polyploids projects is gratefully acknowledged., the authors wish to thank dr. jeffrey endelman (university of wisconsin–madison) for the helpful remarks regarding tetraploid kinship matrices, and dr. heleen bastiaanssen (anthura b.v.) for the helpful feedback on the manuscript., https://cran.r-project.org/package=fitpoly , https://bioss.ac.uk/knowledge/tetramap.html , […]

2016
PMCID: 4765046

[…] but can be included analogous to the effect of the variant xa. the background covariance matrix kbg can be flexibly chosen, such as a global kinship matrix to model relatedness [62] or a local kinship matrix to model cis effects that act on the focal gene [19]. in the experiments, we use the realized relationship matrix [62] as background covariance, thereby adjusting for population […]

2016
PMCID: 4878195

[…] accomplished using mixed model algorithms such as emma (10) or fast-lmm (11). these algorithms essentially perform a t-test for association while correcting for population structure using a kinship matrix based on genotypes. genome-wide significance is determined using simulation, a bonferroni correction, or a false discovery rate (1, 12)., with only 100 inbred strains in the hmdp, […]

2015
PMCID: 4620006

[…] by definition as follows: fij = (qij – qm/(1 – qm), where qij is the probability of ibs for random loci from i and j, and qm is the average probability of ibs for loci from random individuals. pair-kinship coefficients of 0, 0 to 0.1 and 0.1 to 0.5 indicated weak, intermediate, and strong similarity between accessions, respectively [35]. the gd, heterozygosity, and pic were calculated […]

kinship institution(s)
Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Chinahester, MN, USA

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