Last updated: 2024-01-22

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File Version Author Date Message
Rmd 10423d8 Tina Lasisi 2023-05-18 Update to add IBD page
html 10423d8 Tina Lasisi 2023-05-18 Update to add IBD page 
# Load required packages
library(tidyverse)
── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.4     ✔ readr     2.1.5
✔ forcats   1.0.0     ✔ stringr   1.5.1
✔ ggplot2   3.4.4     ✔ tibble    3.2.1
✔ lubridate 1.9.3     ✔ tidyr     1.3.0
✔ purrr     1.0.2     
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
library(patchwork)

knitr::opts_knit$set(root.dir = "..")
knitr::opts_chunk$set(eval = TRUE, echo = FALSE, fig.width = 7, fig.height = 6)

Load data and wrangle

Rows: 44737 Columns: 5
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (4): ID1, POP1, ID2, POP2
dbl (1): IBD_CM_SUM

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
`summarise()` has grouped output by 'POP1'. You can override using the `.groups` argument.
# A tibble: 3 × 3
# Groups:   POP1 [2]
  POP1  POP2  mean_ibd
  <chr> <chr>    <dbl>
1 ASW   ASW     342.  
2 CEU   ASW       5.79
3 CEU   CEU      17.3

Version Author Date
10423d8 Tina Lasisi 2023-05-18

Here we see that there is much higher mean IBD in the ASW sample than expected. After checking for errors, it appears that this has to do with the nature of the HapMap sample. African Ancestry in SW USA (ASW) contains 20 parent-child duos, 13 trios, and 5 families of 2 or more with only 15 unrelated individuals (see link). Given the description of the sample, it seems really important to not use this population as a proxy for African Americans.

Below the filtered data is re-visualized as distributions for different kinship levels.

Version Author Date
10423d8 Tina Lasisi 2023-05-18

Version Author Date
10423d8 Tina Lasisi 2023-05-18

Version Author Date
10423d8 Tina Lasisi 2023-05-18 

    Welch Two Sample t-test

data:  IBD_CM_SUM by POP1
t = 3.6655, df = 122.79, p-value = 0.0003659
alternative hypothesis: true difference in means between group ASW and group CEU is not equal to 0
95 percent confidence interval:
 18.14282 60.74416
sample estimates:
mean in group ASW mean in group CEU 
         49.77737          10.33388

Version Author Date
10423d8 Tina Lasisi 2023-05-18 

R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.2.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Detroit
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] patchwork_1.2.0 lubridate_1.9.3 forcats_1.0.0   stringr_1.5.1  
 [5] dplyr_1.1.4     purrr_1.0.2     readr_2.1.5     tidyr_1.3.0    
 [9] tibble_3.2.1    ggplot2_3.4.4   tidyverse_2.0.0 workflowr_1.7.1

loaded via a namespace (and not attached):
 [1] gtable_0.3.4       xfun_0.41          bslib_0.6.1        processx_3.8.3    
 [5] callr_3.7.3        tzdb_0.4.0         vctrs_0.6.5        tools_4.3.2       
 [9] ps_1.7.5           generics_0.1.3     parallel_4.3.2     fansi_1.0.6       
[13] highr_0.10         pkgconfig_2.0.3    RColorBrewer_1.1-3 lifecycle_1.0.4   
[17] compiler_4.3.2     farver_2.1.1       git2r_0.33.0       munsell_0.5.0     
[21] getPass_0.2-4      httpuv_1.6.13      htmltools_0.5.7    sass_0.4.8        
[25] yaml_2.3.8         later_1.3.2        pillar_1.9.0       crayon_1.5.2      
[29] jquerylib_0.1.4    whisker_0.4.1      cachem_1.0.8       tidyselect_1.2.0  
[33] digest_0.6.34      stringi_1.8.3      labeling_0.4.3     rprojroot_2.0.4   
[37] fastmap_1.1.1      grid_4.3.2         colorspace_2.1-0   cli_3.6.2         
[41] magrittr_2.0.3     utf8_1.2.4         withr_2.5.2        scales_1.3.0      
[45] promises_1.2.1     bit64_4.0.5        timechange_0.2.0   rmarkdown_2.25    
[49] httr_1.4.7         bit_4.0.5          hms_1.1.3          evaluate_0.23     
[53] knitr_1.45         rlang_1.1.3        Rcpp_1.0.12        glue_1.7.0        
[57] rstudioapi_0.15.0  vroom_1.6.5        jsonlite_1.8.8     R6_2.5.1          
[61] fs_1.6.3