title: "Using create statements and referencing local data frames" author: "Edvald Gislason edvald@wuxinextcode.com" date: "2020-10-01" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{GOR Create Statements and Virtual Relations} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8}
In this example, we're going to show how the gor_create
can be used to prepare and construct a query closure. This both reduces repetitions in code, as well as simplifies iterative workflows in GOR.
First load the gorr
package, the tidyverse
package is recommended, but for the sake of simplicity we pick out the ones we're using:
library(gorr)
library(magrittr) # pipe
library(dplyr)
#>
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
Next we make a conn
object for holding information on the API we're connecting to. gor_connect
takes 2 parameters api_key
and project
but if either are left out then it will try to read the environment variables GOR_API_KEY
, and GOR_API_PROJECT
respectively. Here below we have the GOR_API_KEY
environment variable already defined so supplying the function only with a target project suffices. After this we create a query
function/closure so we don't have to reference conn
again:
conn <- gor_connect(project = "ukbb_hg38")
query <- gor_create(conn = conn)
query
#> ── GOR Creation Query ──────────────────────────────────────────────────────────
#> Connection
#> Service Root: https://platform.wuxinextcodedev.com/api/query
#> Project: ukbb_hg38
#> Definitions
#> None
#> Create statements & virtual relations
#> None
Now we can call that function with only the query parameter. Let's search for genes containing BRCA and save the resulting table as a local dataframe mygenes
:
mygenes <- query("gor #genes# | grep BRCA")
mygenes
#> # A tibble: 2 x 4
#> chrom gene_start gene_end gene_symbol
#> <chr> <int> <int> <chr>
#> 1 chr13 32315473 32400266 BRCA2
#> 2 chr17 43044294 43170245 BRCA1
Next we can expand on our previously defined query
function by supplying it back into gor_create
as the replace
parameter. This time we include some definitions using the defs
parameter and then we can alias our local dataframe so that we can reference it in remote queries. In GOR this is called virtual relations:
query <- gor_create(
defs = "def variants = #dbsnp#",
mygenes = mygenes,
replace = query
)
query
#> ── GOR Creation Query ──────────────────────────────────────────────────────────
#> Connection
#> Service Root: https://platform.wuxinextcodedev.com/api/query
#> Project: ukbb_hg38
#> Definitions
#> def variants = #dbsnp#;
#> Create statements & virtual relations
#> mygenes
#> # A tibble: 2 x 4
#> chrom gene_start gene_end gene_symbol
#> <chr> <int> <int> <chr>
#> 1 chr13 32315473 32400266 BRCA2
#> 2 chr17 43044294 43170245 BRCA1
Now that we have our updated query
function, we can use it to gor
our table of genes and join it to the #dbsnp#
table we aliased as variants
in the definitions part above. The result is a list of all variants within each gene in our table
brca_variants <- query("
gor [mygenes] | join -segvar variants
")
brca_variants %>%
group_by(gene_symbol) %>%
summarize(records = n(),
variants = n_distinct(rsids))
#> `summarise()` ungrouping output (override with `.groups` argument)
#> # A tibble: 2 x 3
#> gene_symbol records variants
#> <chr> <int> <int>
#> 1 BRCA1 37150 32933
#> 2 BRCA2 28635 25174
The reason for the difference in # records
and # variants
above can be explained by looking into the data:
target_variant <-
brca_variants %>%
group_by(rsids) %>%
count() %>%
ungroup() %>%
arrange(desc(n)) %>%
head(n = 1) %>%
pull(rsids)
target_variant
#> [1] "rs71071031"
brca_variants %>% filter(rsids == target_variant) %>% select(-distance)
#> # A tibble: 23 x 8
#> chrom gene_start gene_end gene_symbol pos reference allele rsids
#> <chr> <int> <int> <chr> <int> <chr> <chr> <chr>
#> 1 chr13 32315473 32400266 BRCA2 3.24e7 TTTTTTTTTTTTTTT… T rs7107…
#> 2 chr13 32315473 32400266 BRCA2 3.24e7 TTTTTTTTTTTTTTT… T rs7107…
#> 3 chr13 32315473 32400266 BRCA2 3.24e7 TTTTTTTTTTTTTTT… T rs7107…
#> 4 chr13 32315473 32400266 BRCA2 3.24e7 TTTTTTTTTTTTTTT… T rs7107…
#> 5 chr13 32315473 32400266 BRCA2 3.24e7 TTTTTTTTTTTTTTT… T rs7107…
#> 6 chr13 32315473 32400266 BRCA2 3.24e7 TTTTTTTTTTTTTTT… T rs7107…
#> 7 chr13 32315473 32400266 BRCA2 3.24e7 TTTTTTTTTTTTTTT… T rs7107…
#> 8 chr13 32315473 32400266 BRCA2 3.24e7 TTTTTTTTTTTTTTT… T rs7107…
#> 9 chr13 32315473 32400266 BRCA2 3.24e7 TTTTTTTTTTTTTTT… T rs7107…
#> 10 chr13 32315473 32400266 BRCA2 3.24e7 TTTTTTTTTTTTTTTT T rs7107…
#> # … with 13 more rows
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