R/sql code to find the haplotype data from patient's rsIDs
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Last seen 26 days ago

Enter the body of text here Hi, I need r code or sql command to find the correct haplotype and finally get the correct diplotype. I have the below table, from which I need to get single haplotype for each rsID.

NCBI SNP Reference Wild Variant Haplotype Name  Reference Allele    Variant Allele
rs7900194             G G   CYP2C9*8    G   A
rs7900194             G G   CYP2C9*27   G   T
rs1799853             C T   CYP2C9*2    C   T
rs1799853             C T   CYP2C9*35   C   T
rs1799853             C T   CYP2C9*61   C   T
rs1057910             A A   CYP2C9*3    A   C
rs1057910             A A   CYP2C9*18   A   C

Code should be placed in three backticks as shown below

dplyr %>% group_by("NCBI SNP Reference","Wild","Variant") %>% filter(n()>1) 

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

[1] LC_COLLATE=English_India.utf8  LC_CTYPE=English_India.utf8   
[3] LC_MONETARY=English_India.utf8 LC_NUMERIC=C                  
[5] LC_TIME=English_India.utf8    

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

other attached packages:
[1] dplyr_1.1.3     ggplot2_3.4.1   tidyverse_2.0.0

loaded via a namespace (and not attached):
 [1] fansi_1.0.4       withr_2.5.0       utf8_1.2.3        grid_4.2.2       
 [5] R6_2.5.1          lifecycle_1.0.3   gtable_0.3.1      magrittr_2.0.3   
 [9] scales_1.2.1      pillar_1.9.0      rlang_1.1.2       cli_3.6.0        
[13] rstudioapi_0.15.0 generics_0.1.3    vctrs_0.6.4       tools_4.2.2      
[17] glue_1.6.2        munsell_0.5.0     compiler_4.2.2    pkgconfig_2.0.3  
[21] colorspace_2.1-0  tidyselect_1.2.0  tibble_3.2.1
starallele phenoTest • 70 views

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