ld_analysis
sq-96
2021-07-05
Last updated: 2021-07-26
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Knit directory: LD_Analysis/
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Objective
Comparing eigenvalues and eigenvectors of LD matrices calcualted with different subsamples.
Method
Data is from 1000 Genome EUR ancestry (~500 individuals). Samples are randomly splitted into 3 subsets, each has 160 individuals. Using PLINL to alculate LD matrices with variants (MAF > 0.05) in three SCZ loci.
Result
chr15 91416560-91429040
The first ten eigenvalues
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
EUR_sub1 14.507 10.845 0.885 0.744 0.458 0.190 0.135 0.061 0.054 0.037
EUR_sub2 14.503 11.196 0.862 0.605 0.419 0.173 0.082 0.054 0.048 0.015
EUR_sub3 13.488 11.461 1.059 0.815 0.572 0.187 0.130 0.084 0.073 0.058
EUR_All 14.084 11.226 0.874 0.792 0.482 0.188 0.088 0.067 0.055 0.036Pairwise correlation of the ith eigenvectors
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
sub1.vs.sub2 0.990 0.998 0.965 0.961 -0.940 0.947 -0.528 0.379 -0.365 -0.021
sub1.vs.sub3 0.864 0.956 -0.051 -0.216 -0.972 0.868 -0.106 0.137 0.347 0.161
sub2.vs.sub3 0.925 0.972 -0.167 -0.395 0.910 0.912 0.085 -0.503 -0.575 0.004
sub1.vs.All 0.980 0.996 -0.937 -0.905 0.991 0.969 0.904 -0.769 -0.687 0.219
sub2.vs.All 0.998 0.999 -0.958 -0.955 -0.968 0.980 -0.797 -0.698 0.637 -0.131
sub3.vs.All 0.948 0.979 0.389 0.590 -0.977 0.953 -0.206 -0.019 -0.576 0.536Pairwise correlation between two sets of eigenvectors
chr8 4177794-4192544
The first ten eigenvalues
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
EUR_sub1 38.418 29.334 17.410 3.603 2.218 1.479 1.220 1.083 0.939 0.712
EUR_sub2 41.208 27.896 16.586 3.776 2.082 1.514 1.252 1.136 0.987 0.587
EUR_sub3 43.011 28.383 15.097 3.686 2.217 1.173 1.091 0.962 0.817 0.706
EUR_All 40.807 28.743 16.199 3.586 2.177 1.282 1.074 1.032 0.996 0.687Pairwise correlation of the ith eigenvectors
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
sub1.vs.sub2 0.481 -0.815 0.860 -0.952 0.823 0.087 0.021 -0.543 0.517 -0.325
sub1.vs.sub3 0.996 -0.989 0.984 0.920 -0.872 0.477 0.308 -0.690 0.012 0.482
sub2.vs.sub3 0.518 0.769 0.890 -0.835 -0.778 0.735 0.226 0.197 -0.378 -0.321
sub1.vs.All 0.997 -0.996 0.995 -0.992 0.953 0.515 -0.159 0.089 0.298 0.760
sub2.vs.All 0.450 0.842 0.884 0.968 0.927 0.784 0.344 0.491 0.627 -0.101
sub3.vs.All 0.991 0.990 0.995 -0.933 -0.928 0.901 0.718 -0.378 -0.571 0.457Pairwise correlation between two sets of eigenvectors
Heatmap of LD matrix
chr10 18681005-18770105
The first ten eigenvalues
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
EUR_sub1 85.111 63.778 53.515 26.972 11.070 8.549 7.872 3.639 3.398 3.001
EUR_sub2 80.116 68.940 47.786 29.973 11.169 10.196 7.929 4.504 3.271 2.721
EUR_sub3 85.548 69.447 53.013 28.336 8.967 8.474 5.279 3.999 3.307 2.724
EUR_All 81.628 67.213 52.643 28.061 10.654 9.106 6.961 3.648 3.072 3.037Pairwise correlation of the ith eigenvectors
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
sub1.vs.sub2 -0.833 0.618 0.819 -0.934 -0.266 -0.054 -0.424 -0.384 -0.717
sub1.vs.sub3 0.912 0.865 0.917 0.921 0.837 -0.557 -0.256 0.150 -0.652
sub2.vs.sub3 -0.736 0.708 0.844 -0.871 -0.057 0.185 0.875 0.498 0.496
sub1.vs.All 0.970 0.868 0.932 0.972 0.970 -0.636 -0.494 0.496 0.479
sub2.vs.All -0.860 0.836 0.953 -0.965 -0.216 0.214 0.980 -0.869 -0.663
sub3.vs.All 0.956 0.929 0.954 0.953 0.902 0.906 0.871 -0.281 -0.023
[,10]
sub1.vs.sub2 0.404
sub1.vs.sub3 -0.153
sub2.vs.sub3 0.379
sub1.vs.All -0.114
sub2.vs.All 0.378
sub3.vs.All -0.082Pairwise correlation between two sets of eigenvectors
sessionInfo()R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RColorBrewer_1.1-2 plot.matrix_1.6 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 whisker_0.4 knitr_1.33 magrittr_2.0.1
[5] R6_2.5.0 rlang_0.4.11 fansi_0.5.0 highr_0.9
[9] stringr_1.4.0 tools_4.0.4 xfun_0.24 utf8_1.2.1
[13] git2r_0.28.0 jquerylib_0.1.4 htmltools_0.5.1.1 ellipsis_0.3.2
[17] rprojroot_2.0.2 yaml_2.2.1 digest_0.6.27 tibble_3.1.2
[21] lifecycle_1.0.0 crayon_1.4.1 later_1.2.0 sass_0.4.0
[25] vctrs_0.3.8 promises_1.2.0.1 fs_1.5.0 glue_1.4.2
[29] evaluate_0.14 rmarkdown_2.9 stringi_1.6.2 bslib_0.2.5.1
[33] compiler_4.0.4 pillar_1.6.1 jsonlite_1.7.2 httpuv_1.6.1
[37] pkgconfig_2.0.3