var_in_tx: example output of queryOC – variant in transcribed region

var_in_tx: example output of queryOC – variant in transcribed region

var_in_tx

Format

httr GET result

Source

demo run

Note

The value component of 'cookies' was deleted.

Examples

var_in_tx
#> Response [https://run.opencravat.org/submit/annotate?chrom=chr7&pos=140753336&ref_base=A&alt_base=T&annotators=chasmplus_BRCA,pubmed,segway_breast]
#>   Date: 2020-09-07 10:33
#>   Status: 200
#>   Content-Type: application/json; charset=utf-8
#>   Size: 1.31 kB
#> 
str(httr::content(var_in_tx))
#> List of 4
#>  $ pubmed        :List of 2
#>   ..$ n   : int 3194
#>   ..$ term: chr "http://www.ncbi.nlm.nih.gov/pubmed?term=BRAF[TIAB] AND cancer[MH]"
#>  $ segway_breast :List of 2
#>   ..$ breast_myoepithelial_cells: chr "Transcribed"
#>   ..$ breast_vhmec              : chr "Transcribed"
#>  $ chasmplus_BRCA:List of 4
#>   ..$ score     : num 0.159
#>   ..$ transcript: chr "NM_004333.4"
#>   ..$ pval      : num 0.0307
#>   ..$ results   : chr "*NM_004333.4:(0.159:0.0307)"
#>  $ crx           :List of 13
#>   ..$ uid         : chr ""
#>   ..$ chrom       : chr "chr7"
#>   ..$ pos         : int 140753336
#>   ..$ ref_base    : chr "A"
#>   ..$ alt_base    : chr "T"
#>   ..$ note        : chr ""
#>   ..$ coding      : chr "Yes"
#>   ..$ hugo        : chr "BRAF"
#>   ..$ transcript  : chr "ENST00000644969.1"
#>   ..$ so          : chr "missense_variant"
#>   ..$ cchange     : chr "c.1919T>A"
#>   ..$ achange     : chr "p.Val640Glu"
#>   ..$ all_mappings: chr "{\"BRAF\": [[\"\", \"p.Val640Glu\", \"missense_variant\", \"ENST00000288602.11\", \"c.1919T>A\"], [\"\", \"p.Va"| __truncated__