AnnoQR (R Package)
Introduction
This is an R client for performing queries with AnnoQ API.
Installation
Install from GitHub Repo
Make sure you have installed devtools
.
install.packages("devtools")
Then
library(devtools)
` install_github(“USCbiostats/AnnoQR”)`
Function list
- add_query_filter
- add_source
- exists_filter
- init_query_js_body
- keywordsQuery
- perform_search
- query_obj_to_json
- range_filter
- read_config
- regionQuery
- rsidQuery
- term_filter
Examples
Query Variants with ANNOVAR_ensembl_Effect
Annotation
library(AnnoQR)
q = init_query_js_body()
ex = exists_filter("ANNOVAR_ensembl_Effect")
q = add_query_filter(q, ex)
variants = perform_search(q)
variants
Only retrieve ANNOVAR_ensembl_Effect
column
q = add_source(q, c("ANNOVAR_ensembl_Effect"))
variants = perform_search(q)
variants
Query variants field SnpEff_ensembl_Effect
marked as intergenic_region
q = init_query_js_body()
term_f = term_filter('SnpEff_ensembl_Effect' , 'intergenic_region')
q = add_query_filter(q, term_f)
variants = perform_search(q)
variants
Query variants field SnpEff_ensembl_Effect
marked as `intergenic_region with in chromosome 20
q = init_query_js_body()
term_f1 = term_filter('SnpEff_ensembl_Effect' , 'intergenic_region')
term_f2 = term_filter('chr' , '20')
q = add_query_filter(q, term_f1)
q = add_query_filter(q, term_f2)
#q = add_source(q, c('SnpEff_ensembl_Effect'))
variants = perform_search(q)
variants
Query variants with 1000 genome allel count 1000Gp3_AC
larger than 5
q = init_query_js_body()
range_f = range_filter(key='1000Gp3_AC' , gt=5)
q = add_query_filter(q, range_f)
variants = perform_search(q)
variants
Chromosome range query
variants = regionQuery(contig = '20', start=31710367, end=31820367)
variants
rsID query
variant = rsidQuery('rs193031179')
variant
keywordsQuery
keywordsQuery('protein_coding')
Whats Next