obtain AlphaMissense TabixFile from cache, after retrieving the relevant resource if not present there

get_alphamis_txf(cache = BiocFileCache::BiocFileCache(), build = "hg38")

Arguments

cache: An instance of BiocFileCache
build: character(1) defaults to "hg38"

Note

First invocation on a given R deployment will a) request that a cache be built if BiocFileCache has never been used, b) populate the cache with ~600MB of bgzipped tabix-indexed variant-level data.

Examples

ca = BiocFileCache::BiocFileCache()
txf = get_alphamis_txf(ca) # will download if data are not already cached
Rsamtools::yieldSize(txf) = 10L
read.delim(text=Rsamtools::scanTabix(txf)[[1]], h=FALSE) 
#>      V1    V2 V3 V4   V5     V6                V7  V8     V9           V10
#> 1  chr1 69094  G  T hg38 Q8NH21 ENST00000335137.4 V2L 0.2937 likely_benign
#> 2  chr1 69094  G  C hg38 Q8NH21 ENST00000335137.4 V2L 0.2937 likely_benign
#> 3  chr1 69094  G  A hg38 Q8NH21 ENST00000335137.4 V2M 0.3296 likely_benign
#> 4  chr1 69095  T  C hg38 Q8NH21 ENST00000335137.4 V2A 0.2609 likely_benign
#> 5  chr1 69095  T  A hg38 Q8NH21 ENST00000335137.4 V2E 0.2922 likely_benign
#> 6  chr1 69095  T  G hg38 Q8NH21 ENST00000335137.4 V2G 0.2030 likely_benign
#> 7  chr1 69097  A  G hg38 Q8NH21 ENST00000335137.4 T3A 0.0929 likely_benign
#> 8  chr1 69097  A  C hg38 Q8NH21 ENST00000335137.4 T3P 0.1264 likely_benign
#> 9  chr1 69097  A  T hg38 Q8NH21 ENST00000335137.4 T3S 0.0979 likely_benign
#> 10 chr1 69098  C  A hg38 Q8NH21 ENST00000335137.4 T3N 0.1121 likely_benign