Last updated: 2022-05-19

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File Version Author Date Message
Rmd 434e8b9 Marek Cmero 2022-05-19 Added in silico mixtures to navigation
html ff1f665 Marek Cmero 2022-05-19 Build site.
Rmd 572a31d Marek Cmero 2022-05-19 Added initial results from in silico mixture experiment

In this experiment, the duplex reads from NanoSeq MB2 rep 1 from E coli K12 was mixed (in silico) at 10x depth with the duplex reads from NanoSeq MB2 (MGI) from E coli BL21 at 90x depth creating a 10% mixed genome. There are >33k SNP and INDEL differences between the E coli species, so we would expect to find approximately this many SNPs at the mixture frequency.

library(ggplot2)
library(data.table)
library(dplyr)
library(here)
library(tibble)
library(stringr)
library(Rsamtools)
library(GenomicRanges)
library(seqinr)
library(readxl)
library(patchwork)
library(RColorBrewer)
library(UpSetR)
library(vcfR)
source(here('code/load_data.R'))
variant_dir <- here('data/mixtures')
var_df <- load_variants(variant_dir, 'NanoMB2-0.1')
tmp <- var_df$Sample1 %>% str_split(':') %>% lapply(., function(x){as.numeric(x[5:6])}) 
var_df$RD <- lapply(tmp, head, 1) %>% unlist()
var_df$AD <- lapply(tmp, tail, 1) %>% unlist()

var_df$VAF <- var_df$AD / (var_df$AD + var_df$RD)
var_df <- var_df[var_df$VAF < 0.3,] # filter low frequency VAFs

VAFs (10% mixture)

NanoSeq MB2

  • 10x – K12
  • 90x – BL21
ggplot(var_df, aes(VAF)) +
    geom_histogram(bins = 50) +
    theme_minimal() +
    scale_x_continuous(breaks = seq(0, 1, 0.1), limits = c(0, 1))

Version Author Date
ff1f665 Marek Cmero 2022-05-19 

sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /stornext/System/data/apps/R/R-4.0.5/lib64/R/lib/libRblas.so
LAPACK: /stornext/System/data/apps/R/R-4.0.5/lib64/R/lib/libRlapack.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] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] vcfR_1.12.0          UpSetR_1.4.0         RColorBrewer_1.1-2  
 [4] patchwork_1.1.1      readxl_1.3.1         seqinr_4.2-8        
 [7] Rsamtools_2.6.0      Biostrings_2.58.0    XVector_0.30.0      
[10] GenomicRanges_1.42.0 GenomeInfoDb_1.26.7  IRanges_2.24.1      
[13] S4Vectors_0.28.1     BiocGenerics_0.36.1  stringr_1.4.0       
[16] tibble_3.1.5         here_1.0.1           dplyr_1.0.7         
[19] data.table_1.14.0    ggplot2_3.3.5        workflowr_1.6.2     

loaded via a namespace (and not attached):
 [1] sass_0.4.0             viridisLite_0.4.0      splines_4.0.5         
 [4] jsonlite_1.7.2         bslib_0.3.0            assertthat_0.2.1      
 [7] memuse_4.2-1           highr_0.9              GenomeInfoDbData_1.2.4
[10] cellranger_1.1.0       yaml_2.2.1             pillar_1.6.4          
[13] lattice_0.20-44        glue_1.4.2             digest_0.6.27         
[16] promises_1.2.0.1       colorspace_2.0-0       Matrix_1.3-2          
[19] htmltools_0.5.2        httpuv_1.6.3           plyr_1.8.6            
[22] pkgconfig_2.0.3        zlibbioc_1.36.0        purrr_0.3.4           
[25] scales_1.1.1           whisker_0.4            later_1.3.0           
[28] BiocParallel_1.24.1    git2r_0.28.0           mgcv_1.8-35           
[31] farver_2.1.0           generics_0.1.1         ellipsis_0.3.2        
[34] withr_2.4.2            magrittr_2.0.1         crayon_1.4.2          
[37] evaluate_0.14          fs_1.5.0               fansi_0.5.0           
[40] nlme_3.1-152           MASS_7.3-53.1          vegan_2.5-7           
[43] tools_4.0.5            lifecycle_1.0.1        munsell_0.5.0         
[46] cluster_2.1.2          ade4_1.7-18            compiler_4.0.5        
[49] jquerylib_0.1.4        rlang_0.4.12           grid_4.0.5            
[52] RCurl_1.98-1.3         labeling_0.4.2         bitops_1.0-7          
[55] rmarkdown_2.11         gtable_0.3.0           DBI_1.1.1             
[58] R6_2.5.1               gridExtra_2.3          knitr_1.33            
[61] pinfsc50_1.2.0         fastmap_1.1.0          utf8_1.2.2            
[64] rprojroot_2.0.2        permute_0.9-5          ape_5.5               
[67] stringi_1.7.5          Rcpp_1.0.7             vctrs_0.3.8           
[70] tidyselect_1.1.1       xfun_0.22