Implement support for custom SNP sets#10
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rnmitchell
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Apr 22, 2026
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| shinyFileChoose(input, "sample_GetFile", roots=volumes, session=session) | ||
| samplefile = reactive({parseFilePaths(volumes, input$sample_GetFile)}) | ||
| roots = c(home="~", wd=".") | ||
| shinyFileChoose(input, "sample_GetFile", roots=roots, session=session, defaultRoot="home") | ||
| samplefile = reactive({parseFilePaths(roots, input$sample_GetFile)}) |
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changing to have file picker default to home directory instead of volumes dir
… if needed for conditioning)
rnmitchell
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May 11, 2026
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| output$assay_choice = renderUI({ | ||
| selectInput("assay_choice", tags$span("Select Assay", tags$span(icon( | ||
| name = "question-circle", | ||
| ) | ||
| ) |> | ||
| add_prompt(message = "Select assay used to develop genotypes", position = "right") | ||
| ), c("Kintelligence", "Custom")) | ||
| }) | ||
| output$assay_GetFile = renderUI({ | ||
| fluidRow(column(10,shinyFilesButton("assay_GetFile", "Select a custom SNP positions file" , | ||
| title = "Select a custom SNP positions file", multiple = FALSE, | ||
| buttonType = "default", class = NULL), | ||
| tags$span( | ||
| icon( | ||
| name = "question-circle", | ||
| ) | ||
| ) |> | ||
| add_prompt(message = "File containing chromosomal locations for custom SNP panels.\nThis is not required if using the Kintelligence assay.\nColumns required: rsID, chromosome (e.g. 1, 2, 3,), and position (GRCh37).", position = "right") | ||
| )) | ||
| }) | ||
| output$assay_text = renderUI({ | ||
| textOutput("assay_file") | ||
| }) |
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drop-down menu for "kintelligence" or "custom". If select custom, file selector appears to select file with SNP positions information.
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| withProgress(message = "Loading References", value = 0, { | ||
| if (file.exists(glue("{refs()}/EFM_references.rda"))) { | ||
| load(glue("{refs()}/EFM_references.rda")) |
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searches first for .rda file
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| showModal(modalDialog( | ||
| title = "Input Error", | ||
| "Please provide reference genotypes before proceeding.", | ||
| easyClose = TRUE, | ||
| footer = modalButton("Dismiss") | ||
| )) | ||
| } | ||
| } else if (!isTruthy(input$cond) & !isTruthy(input$uncond)) { | ||
| showModal(modalDialog( | ||
| title = "Input Error", | ||
| "Please select either an Unconditioned or Conditioned analysis (or both!) before proceeding.", | ||
| easyClose = TRUE, | ||
| footer = modalButton("Dismiss") | ||
| )) | ||
| } else { |
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improved error handling using pop-up windows.
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| withProgress(message = "Loading Allele Frequency Data", value = 0, { | ||
| freq_both = ifelse(!isTruthy(freq()$datapath), input$uploadfreq, freq()$datapath) | ||
| freq_major = ifelse(!isTruthy(freq_major()$datapath), input$uploadfreq_major, freq_major()$datapath) | ||
| freq_minor = ifelse(!isTruthy(freq_minor()$datapath), input$uploadfreq_minor, freq_minor()$datapath) | ||
| popFreq = load_freq(input$twofreqs, freq_both, freq_major, freq_minor) |
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now loads the frequency data before looping through each sample in manifest (therefore only loads freq data once).
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| lcol = grep("rsid|marker|locus|snp", colname, ignore.case=TRUE, value=TRUE) | ||
| chrcol = grep("chr", colname, ignore.case=TRUE, value=TRUE) | ||
| poscol = grep("pos", colname, ignore.case=TRUE, value=TRUE) |
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more flexibility with column names
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| format_ref = function(refData, refid, refs) { | ||
| if (is.numeric(refid)) { | ||
| ref_int = names(refData)[refid] | ||
| } else { | ||
| ref_int = refid | ||
| } | ||
| ref_profile = euroformix::tableReader(glue("{refs}/EFM_references.csv")) %>% | ||
| filter(.data$Sample.Name == ref_int) | ||
| #' @importFrom data.table fread | ||
| format_ref = function(refid, refs) { | ||
| ref_profile = data.frame(fread(glue("{refs}/EFM_references.csv"))) %>% | ||
| filter(.data$Sample.Name == refid) |
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Removed legacy code that is no longer used; converted to fread() function for fast reading of file.
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| read_in_freq = function(freq){ | ||
| #efmaf=fread(freq, header=T, sep=",") | ||
| tab=data.frame(freq) |
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Rewrite of EFM freqImport() function to improve speed
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| if (!file.exists(glue("{write_path}/rda_files/{sample}.rda")) | !(keep_bins)) { | ||
| evidData = create_evid(sample, replicate, snps_input) | ||
| dir.create(file.path(write_path, "rda_files"), showWarnings = FALSE, recursive=TRUE) | ||
| save(evidData, file=glue("{write_path}/rda_files/{sample}.rda")) | ||
| } else { | ||
| load(glue("{write_path}/rda_files/{sample}.rda")) | ||
| } |
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Save SNP binned data as .rda file
| #' @export | ||
| #' | ||
| run_mixder_ancestry = function(sample_manifest=NULL, sample=NULL, replicate=NULL, sample_reports = getwd(), output = "output", refpath=NULL, refs=NULL, mixdeconv=TRUE, uncond=TRUE, cond=FALSE, sets=10, dynamicAT=0.015, staticAT=10, minimum_snps=6000, A1_threshold=0.99, A2_threshold=0.6, minor_contrib_threshold=FALSE, keep_bins=TRUE, snps, pcagroups) { | ||
| run_mixder_ancestry = function(sample_manifest=NULL, sample=NULL, replicate="", sample_reports = getwd(), output = "output", refpath=NULL, refs=NULL, mixdeconv=TRUE, uncond=TRUE, cond=FALSE, sets=10, dynamicAT=0.015, staticAT=10, minimum_snps=6000, A1_threshold=0.99, A2_threshold=0.6, minor_contrib_threshold=FALSE, keep_bins=TRUE, snps="ancestry", pcagroups="superpopulations") { |
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Added default values
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| if (dynamicAT != 0) { | ||
| message("creating AT table<br/>") | ||
| attable = process_kinreport(id, replicate_id, kinpath, dynamicAT, staticAT) | ||
| } else { | ||
| attable = staticAT | ||
| } |
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If only static AT is applied, then just the single AT value can be used (a table does not need to be created).
rnmitchell
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May 12, 2026
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| if (!isTruthy(samplefile()$datapath)) { | ||
| showModal(modalDialog( | ||
| title = "Input Error", | ||
| "Please provide a sample manifest before proceeding.", | ||
| easyClose = TRUE, | ||
| footer = modalButton("Dismiss") | ||
| )) | ||
| } else if (!isTruthy(kin_inpath())) { |
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updated error handling for missing files in Shiny app- pop-up window will appear stating the problem instead of random closing of the app
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This MR will implement support for custom, larger SNP sets, including changes to increase the speed of uploading data (and formatting appropriately for EFM).