In davemcg/SeeGEM: Integrate 'GEMINI' (and 'peddy') Output into Interactive Html Document

opts_chunk$set(echo = F,
               warning = F,
               message = F)

# decorate data, or return as given
if (params$decorate){
  document_data <- See_GEM_formatter(GEMINI_data)
} else{
  document_data <- GEMINI_data}

r params$sample_name {.tabset}

GEMINI Variation

DT::datatable(document_data$GEMINI_data, 
              width = params$table_width, 
              escape = FALSE,
              rownames = F, 
              class='compact', 
              filter='bottom',
              extensions = c('Buttons','FixedHeader', 'ColReorder'),
              options = list(columnDefs=list(list(targets=document_data$neg_core_index-1, visible = FALSE)),
                             pageLength = 15,
                             scrollX = TRUE,
                             fixedHeader = TRUE,
                             colReorder = TRUE,
                             lengthMenu = list(c(5, 15, 30, 60, 100, -1), list('5', '15', '30', '60', '100', 'All')),
                             dom = 'Bfrtip',
                             buttons = list(list(extend = 'pageLength'),
                                            list(extend = 'colvis', collectionLayout='four-column'),
                                            list(extend = 'colvisGroup', text='Core Fields', 
                                                 hide = paste(document_data$neg_core_index-1, collapse = ','), 
                                                 show = paste(document_data$core_index-1, collapse = ',')),
                                            list(extend = 'colvisGroup', text='Family Genotypes', 
                                                 hide = paste(document_data$neg_genotypes-1, collapse = ','), 
                                                 show = paste(document_data$genotypes-1, collapse = ',')),
                                            list(extend = 'colvisGroup', text='In Silico Fields', 
                                                 hide = paste(document_data$neg_in_silico_index-1, collapse = ','), 
                                                 show = paste(document_data$in_silico_index-1, collapse = ',')),
                                            list(extend='colvisGroup', text='Show All', show = ':hidden' )))) %>% 
  DT::formatStyle(columns = c('Color'), target = 'row', backgroundColor = DT::styleEqual(c(0, 1, 2), c('#ffffff', '#fff0dd', '#ffdddd'))) 

Info

This report is auto-generated with the See GEM R package on r strftime(Sys.time(), format = "%B %d, %Y")

The analyst for this report populated the information in this dynamic documents with a variety of GEMINI queries.

FAQ:

• What does it mean if a variant is marked in red?
• This means that the variant has an impact severity of HIGH or is marked as pathogenic in ClinVar and has a gnomAD population allele frequency less than 1%.
• Orange?
• MED impact severity

WARNINGS/LIMITATIONS

• This document is only a tool to aid identification of causative variant(s)
• The in silico consequences (e.g. stop gained, synonymous) are automatically calculated, and for a variety of reasons, may not be accurate.
• The causative variants may not be present in this document

davemcg/SeeGEM documentation built on May 5, 2019, 1:34 a.m.