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()
The Broad Institute SNP Annotation and Proxy Search
- See http://www.broadinstitute.org/mpg/snap/index.php for more details
- Relavant functions:
ld_search()
NCBI's dbSNP SNP database
- See https://www.ncbi.nlm.nih.gov/snp for more details
- Relavant functions:
ncbi_snp_query()ncbi_snp_query2()
Install
Install from CRAN
install.packages("rsnps")Or dev version
install.packages("devtools")
devtools::install_github("ropensci/rsnps")library("rsnps")Search for SNPs in Linkage Disequilibrium
Using the Broad Institute data
tmp <- ld_search("rs420358")#> Querying SNAP...
#> Querying NCBI for up-to-date SNP annotation information...
#> Done!head(tmp)#> $rs420358
#> Proxy SNP Distance RSquared DPrime GeneVariant GeneName
#> 4 rs420358 rs420358 0 1.000 1.000 INTERGENIC N/A
#> 5 rs442418 rs420358 122 1.000 1.000 INTERGENIC N/A
#> 8 rs718223 rs420358 1168 1.000 1.000 INTERGENIC N/A
#> 6 rs453604 rs420358 2947 1.000 1.000 INTERGENIC N/A
#> 3 rs372946 rs420358 -70 0.943 1.000 INTERGENIC N/A
#> 1 rs10889290 rs420358 3987 0.800 1.000 INTERGENIC N/A
#> 2 rs10889291 rs420358 4334 0.800 1.000 INTERGENIC N/A
#> 7 rs4660403 rs420358 7021 0.800 1.000 INTERGENIC N/A
#> GeneDescription Major Minor MAF NObserved marker_NCBI organism_NCBI
#> 4 N/A C A 0.167 120 rs420358 Homo sapiens
#> 5 N/A C T 0.167 120 rs442418 Homo sapiens
#> 8 N/A A G 0.167 120 rs718223 Homo sapiens
#> 6 N/A A G 0.167 120 rs453604 Homo sapiens
#> 3 N/A G C 0.175 120 rs372946 Homo sapiens
#> 1 N/A G A 0.200 120 rs10889290 Homo sapiens
#> 2 N/A C T 0.200 120 rs10889291 Homo sapiens
#> 7 N/A A G 0.200 120 rs4660403 Homo sapiens
#> chromosome_NCBI assembly_NCBI alleles_NCBI minor_NCBI maf_NCBI bp_NCBI
#> 4 1 GRCh38.p2 G/T <NA> <NA> 40341239
#> 5 1 GRCh38.p2 A/G T 0.0723 40341361
#> 8 1 GRCh38.p2 A/G G 0.0723 40342407
#> 6 1 GRCh38.p2 A/G G 0.0727 40344186
#> 3 1 GRCh38.p2 C/G <NA> <NA> 40341169
#> 1 1 GRCh38.p2 A/G A 0.0841 40345226
#> 2 1 GRCh38.p2 C/T T 0.0839 40345573
#> 7 1 GRCh38.p2 A/G G 0.0827 40348260Using NCBI dbSNP data
SNPs <- c("rs332", "rs420358", "rs1837253", "rs1209415715", "rs111068718")
ncbi_snp_query(SNPs)#> Query Chromosome Marker Class Gene Alleles Major
#> 1 rs332 7 rs121909001 in-del CFTR -/TTT <NA>
#> 2 rs420358 1 rs420358 snp <NA> G,T G
#> 3 rs1837253 5 rs1837253 snp <NA> C/T C
#> 4 rs111068718 <NA> rs111068718 microsatellite <NA> (GT)21/24 <NA>
#> Minor MAF BP AncestralAllele
#> 1 <NA> NA 117559593 <NA>
#> 2 T NA 40341239 T,T,T,T,T,T
#> 3 T 0.3822 111066174 T,T,T,T,T,T
#> 4 <NA> NA NA <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 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 TTphenotypes() function
out <- phenotypes(userid=1)
out$phenotypes$`Hair Type`#> $phenotype_id
#> [1] 16
#>
#> $variation
#> [1] "straight"Meta
- Please report any issues or bugs.
- License: MIT
- Get citation information for
rsnspsin R doingcitation(package = 'rsnps') - Please note that this project is released with a Contributor Code of Conduct.
By participating in this project you agree to abide by its terms.