ALPHAMISSENSE_RECORD is a constant identifier
corresponding to the default version of the AlphaMissense
resource to use.
am_browse() opens a web browser at the Zenodo record
for the AlphaMissense data.
am_available() reports available datasets in the
record.
am_data() retrieves a single key from the the
AlpahMissense Zenodo site and parses the file into a DuckDB
database.
Usage
ALPHAMISSENSE_RECORD
am_browse(record = ALPHAMISSENSE_RECORD)
am_available(record = ALPHAMISSENSE_RECORD, bfc = BiocFileCache())
am_data(
key,
record = ALPHAMISSENSE_RECORD,
bfc = BiocFileCache(),
as = c("tbl", "tsv")
)Arguments
- record
character(1) Zenodo record for the AlphaMissense data resources.
- bfc
an object returned by
BiocFileCache()representing the location where downloaded files and the parsed database will be stored. The default is the 'global' BiocFileCache.- key
a character(1) 'key' from the result of
am_available(), or a single row of the tibble returned byam_available().- as
chracter(1) type of return value.
"tbl": a dbplyr tbl representation of the database resource."tsv": path to the tsv.gz file representing the resource and downloaded from Zenodo
Value
am_available() returns a tibble with columns key,
size, and link. The meaning of key must be determined with
reference to the information at am_browse().
am_data() returns a dbplyr (database) tibble
represented the downloaded and parsed file. Fields in the
database are as described on the Zenodo resource page.
Details
ALPHAMISSENSE_RECORD can be set before the package is
loaded with the environment variable of the same name, e.g.,
Sys.setenv(ALPHAMISSENSE_RECORD = "10813168"). The default is
the most recent version (version 3) as checked on 11 April,
2024.
am_data() uses BiocFileCache to download and store the
file and the corresponding DuckDB database.
Examples
ALPHAMISSENSE_RECORD
#> [1] "10813168"
if (interactive())
am_browse()
am_available()
#> # A tibble: 7 × 6
#> record key size cached filename link
#> <chr> <chr> <dbl> <lgl> <chr> <chr>
#> 1 10813168 gene_hg38 253636 TRUE AlphaMissense_gene… http…
#> 2 10813168 isoforms_hg38 1177361934 FALSE AlphaMissense_isof… http…
#> 3 10813168 isoforms_aa_substitutions 2461351945 FALSE AlphaMissense_isof… http…
#> 4 10813168 hg38 642961469 TRUE AlphaMissense_hg38… http…
#> 5 10813168 hg19 622293310 FALSE AlphaMissense_hg19… http…
#> 6 10813168 gene_hg19 243943 FALSE AlphaMissense_gene… http…
#> 7 10813168 aa_substitutions 1207278510 TRUE AlphaMissense_aa_s… http…
am_data("hg38")
#> # Source: table<hg38> [?? x 10]
#> # Database: DuckDB v1.1.1 [mtmorgan@Darwin 23.6.0:R 4.5.0//Users/mtmorgan/Library/Caches/org.R-project.R/R/BiocFileCache/121787f1dafbc_121787f1dafbc]
#> CHROM POS REF ALT genome uniprot_id transcript_id protein_variant
#> <chr> <dbl> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 chr1 69094 G T hg38 Q8NH21 ENST00000335137.4 V2L
#> 2 chr1 69094 G C hg38 Q8NH21 ENST00000335137.4 V2L
#> 3 chr1 69094 G A hg38 Q8NH21 ENST00000335137.4 V2M
#> 4 chr1 69095 T C hg38 Q8NH21 ENST00000335137.4 V2A
#> 5 chr1 69095 T A hg38 Q8NH21 ENST00000335137.4 V2E
#> 6 chr1 69095 T G hg38 Q8NH21 ENST00000335137.4 V2G
#> 7 chr1 69097 A G hg38 Q8NH21 ENST00000335137.4 T3A
#> 8 chr1 69097 A C hg38 Q8NH21 ENST00000335137.4 T3P
#> 9 chr1 69097 A T hg38 Q8NH21 ENST00000335137.4 T3S
#> 10 chr1 69098 C A hg38 Q8NH21 ENST00000335137.4 T3N
#> # ℹ more rows
#> # ℹ 2 more variables: am_pathogenicity <dbl>, am_class <chr>
## close the connection opened when adding the data
db_disconnect()