rsnps

NOTE

rsnps used to be ropensnp

Data sources

This set of functions/package accesses data from:

openSNP.org
- https://opensnp.org
- See documentation on the openSNP API https://opensnp.org/faq#api
- See blog post about their API http://opensnp.wordpress.com/2012/01/18/some-progress-on-the-api-json-endpoints
- Relavant functions:
  - allgensnp(), allphenotypes(), annotations(), download_users(), fetch_genotypes(), genotypes(), phenotypes(), phenotypes_byid(), users()
NCBI’s dbSNP SNP database
- See https://www.ncbi.nlm.nih.gov/snp for more details
- Relavant functions:
  - ncbi_snp_query()
  - ncbi_snp_query2()
  - ncbi_snp_summary()

Install

Install from CRAN

install.packages("rsnps")

Or dev version

install.packages("devtools")
devtools::install_github("ropensci/rsnps")

library("rsnps")

Using NCBI dbSNP data

SNPs <- c("rs332", "rs420358", "rs1837253", "rs1209415715", "rs111068718")
ncbi_snp_query(SNPs)

#>          Query Chromosome       Marker  Class Gene Alleles Major Minor
#> 1        rs332          7  rs121909001 in-del CFTR   -/TTT  <NA>  <NA>
#> 2     rs420358          1     rs420358    snp CFTR   A,G,T     A     G
#> 3    rs1837253          5    rs1837253    snp CFTR     C/T     C     T
#> 4 rs1209415715          9 rs1209415715    snp CFTR     C,T     C     T
#>      MAF        BP AncestralAllele
#> 1     NA 117559593            <NA>
#> 2     NA 117559593     T,T,T,T,T,T
#> 3 0.3822 117559593     T,T,T,T,T,T
#> 4     NA 117559593            <NA>

Using openSNP data

genotypes() function

genotypes('rs9939609', userid='1,6,8', df=TRUE)

#>    snp_name snp_chromosome snp_position                 user_name user_id
#> 1 rs9939609             16     53786615 Bastian Greshake Tzovaras       1
#> 2 rs9939609             16     53786615              Nash Parovoz       6
#> 3 rs9939609             16     53786615         Samantha B. Clark       8
#>   genotype_id genotype
#> 1           9       AT
#> 2           5       AT
#> 3           2       TT

phenotypes() function

out <- phenotypes(userid=1)
out$phenotypes$`Hair Type`

#> $phenotype_id
#> [1] 16
#> 
#> $variation
#> [1] "straight"

rsnps

NOTE

Data sources

Install

Using NCBI dbSNP data

Using openSNP data

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