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View Code? Open in Web Editor NEWShiny application for interacting with GA4GH-based data servers
Home Page: http://bioconductor.org/packages/GA4GHshiny/
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elizemikuga4ghshiny's Issues
Search genomic variants by file with genomic locations
The user uploads a text file containing genomic locations. File format should be tabular containing positional fields Reference Name, Start and End. Each line represents a genomic location.
Add error message when "start" is greater than "end" in input Reference Name
If the "start" is greater than "end" in input Reference Name, an error occurs. This error should appear in a message asking to the user to insert numbers of "end" always greater or equal to "start".
The error returns:
'select()' returned 1:1 mapping between keys and columns
No encoding supplied: defaulting to UTF-8.
Warning: Error in request.post: 'request.post()' failed:
URL: http://1kgenomes.ga4gh.org/variants/search
HTTP error: Client error: (400) Bad Request
Server error: {"errorCode": 700526180, "message": "Bad request"}
Stack trace (innermost first):
110: request.post
109: searchVariants
108: eventReactiveHandler [/home/elizabeth/GA4GHshiny/R/server.R#59]
88: variants
87: exprFunc [/home/elizabeth/GA4GHshiny/R/server.R#82]
86: widgetFunc
85: func
84: origRenderFunc
83: renderFunc
82: origRenderFunc
81: output$dt.variants
4: <Anonymous>
3: do.call
2: print.shiny.appobj
1: <Promise>
Session_info
devtools::session_info()
Session info -------------------------------------------------------------------------------------------------------------------------
setting value
version R version 3.4.1 (2017-06-30)
system x86_64, linux-gnu
ui RStudio (1.0.153)
language (EN)
collate en_US.UTF-8
tz America/Sao_Paulo
date 2017-10-09
Packages -----------------------------------------------------------------------------------------------------------------------------
package * version date source
AnnotationDbi * 1.39.3 2017-09-04 Bioconductor
assertthat 0.2.0 2017-04-11 CRAN (R 3.4.1)
base * 3.4.1 2017-08-30 local
bindr 0.1 2016-11-13 CRAN (R 3.4.1)
bindrcpp 0.2 2017-06-17 CRAN (R 3.4.1)
Biobase * 2.37.2 2017-09-04 Bioconductor
BiocGenerics * 0.23.1 2017-09-11 Bioconductor
BiocParallel 1.11.8 2017-09-04 Bioconductor
biomaRt 2.33.4 2017-09-04 Bioconductor
Biostrings 2.45.4 2017-09-04 Bioconductor
bit 1.1-12 2014-04-09 CRAN (R 3.4.1)
bit64 0.9-7 2017-05-08 CRAN (R 3.4.1)
bitops 1.0-6 2013-08-17 CRAN (R 3.4.1)
blob 1.1.0 2017-06-17 CRAN (R 3.4.1)
BSgenome 1.45.3 2017-09-28 Bioconductor
compiler 3.4.1 2017-08-30 local
curl 2.8.1 2017-07-21 CRAN (R 3.4.1)
datasets * 3.4.1 2017-08-30 local
DBI 0.7 2017-06-18 CRAN (R 3.4.1)
DelayedArray 0.3.21 2017-09-28 Bioconductor
devtools 1.13.3 2017-08-02 CRAN (R 3.4.1)
digest 0.6.12 2017-01-27 CRAN (R 3.4.1)
dplyr 0.7.3 2017-09-09 CRAN (R 3.4.1)
DT 0.2 2016-08-09 CRAN (R 3.4.1)
GA4GHclient * 1.1.1 2017-09-04 Bioconductor
GA4GHshiny * 0.99.8 2017-10-09 Bioconductor
GenomeInfoDb * 1.13.4 2017-09-04 Bioconductor
GenomeInfoDbData 0.99.1 2017-09-04 Bioconductor
GenomicAlignments 1.13.6 2017-09-28 Bioconductor
GenomicFeatures * 1.29.11 2017-09-28 Bioconductor
GenomicRanges * 1.29.14 2017-09-28 Bioconductor
glue 1.1.1 2017-06-21 CRAN (R 3.4.1)
graphics * 3.4.1 2017-08-30 local
grDevices * 3.4.1 2017-08-30 local
grid 3.4.1 2017-08-30 local
htmltools 0.3.6 2017-04-28 CRAN (R 3.4.1)
htmlwidgets 0.9 2017-07-10 CRAN (R 3.4.1)
httpuv 1.3.5 2017-07-04 CRAN (R 3.4.1)
httr 1.3.1 2017-08-20 CRAN (R 3.4.1)
IRanges * 2.11.17 2017-09-28 Bioconductor
jsonlite 1.5 2017-06-01 CRAN (R 3.4.1)
lattice 0.20-35 2017-03-25 CRAN (R 3.4.1)
magrittr 1.5 2014-11-22 CRAN (R 3.4.1)
Matrix 1.2-11 2017-08-21 CRAN (R 3.4.1)
matrixStats 0.52.2 2017-04-14 CRAN (R 3.4.1)
memoise 1.1.0 2017-04-21 CRAN (R 3.4.1)
methods * 3.4.1 2017-08-30 local
mime 0.5 2016-07-07 CRAN (R 3.4.1)
miniUI 0.1.1 2016-01-15 CRAN (R 3.4.1)
openxlsx 4.0.17 2017-03-23 CRAN (R 3.4.1)
org.Hs.eg.db * 3.4.1 2017-09-04 Bioconductor
parallel * 3.4.1 2017-08-30 local
pkgconfig 2.0.1 2017-03-21 CRAN (R 3.4.1)
prettyunits 1.0.2 2015-07-13 CRAN (R 3.4.1)
progress 1.1.2 2016-12-14 CRAN (R 3.4.1)
purrr 0.2.3 2017-08-02 CRAN (R 3.4.1)
R6 2.2.2 2017-06-17 CRAN (R 3.4.1)
Rcpp 0.12.13 2017-09-28 CRAN (R 3.4.1)
RCurl 1.95-4.8 2016-03-01 CRAN (R 3.4.1)
rlang 0.1.2 2017-08-09 CRAN (R 3.4.1)
Rsamtools 1.29.1 2017-09-04 Bioconductor
RSQLite 2.0 2017-06-19 CRAN (R 3.4.1)
rtracklayer 1.37.3 2017-09-04 Bioconductor
S4Vectors * 0.15.8 2017-09-28 Bioconductor
shiny * 1.0.5 2017-08-23 CRAN (R 3.4.1)
shinyjs 0.9.1 2017-06-29 CRAN (R 3.4.1)
shinythemes 1.1.1 2016-10-12 CRAN (R 3.4.1)
stats * 3.4.1 2017-08-30 local
stats4 * 3.4.1 2017-08-30 local
stringi 1.1.5 2017-04-07 CRAN (R 3.4.1)
stringr 1.2.0 2017-02-18 CRAN (R 3.4.1)
SummarizedExperiment 1.7.9 2017-09-28 Bioconductor
tibble 1.3.4 2017-08-22 CRAN (R 3.4.1)
tidyr 0.7.1 2017-09-01 CRAN (R 3.4.1)
tools 3.4.1 2017-08-30 local
TxDb.Hsapiens.UCSC.hg19.knownGene * 3.2.2 2017-09-04 Bioconductor
utils * 3.4.1 2017-08-30 local
VariantAnnotation 1.23.8 2017-09-04 Bioconductor
withr 2.0.0 2017-07-28 CRAN (R 3.4.1)
XML 3.98-1.9 2017-06-19 CRAN (R 3.4.1)
xtable 1.8-2 2016-02-05 CRAN (R 3.4.1)
XVector 0.17.1 2017-09-04 Bioconductor
yaml 2.1.14 2016-11-12 CRAN (R 3.4.1)
zlibbioc
Fix HGVS nomenclatures
See: http://varnomen.hgvs.org/
Create unit tests for each case.
Search for variants in all variant sets
Add All option for Variant Sets popup. When selected, app should iterate over all variant sets (VCFs) searching for variants. Result table should have a Variant Set column.
Fix uploaded files on the interface which contains blanks
In the column option Gene Symbols File, is uploaded a plain text file containing list of Gene Symbols (one gene per line) to search for variants, the function fileInput()should read the file to search the genes in Variants( DT::dataTableOutput("dt.variants"),) ignoring or removing blanks that contain in the file.
Remove unnecessary columns from result table
@benilton, which columns should be removed from result table?
Add Help tab
Add Help tab. This tab should be displayed first instead of Search Veriants tab. Search variants should be renamed to Genomic Variants tab. After search process is completed, application should display Genomic Variants tab.
Remove About tab.
Genomic Variants and Beacon Network tabs should be disabled at beginning.
Help text:
# TODO
Add button for download result table
User clicks on Download Results button. Application generates a text file in tabular format containing all fields in result table. This button should be disabled when there is no result table.
Add loading message dialog
Trigger a loading message dialog when User click on "Search". The message should not have any button. The message dialog should disappear at the search process is completed. The text message should be Searching for genomic variants, please wait.
Shiny element: https://shiny.rstudio.com/reference/shiny/latest/modalDialog.html
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