@sjcrh/proteinpaint-server 2.122.0 → 2.124.0

package/utils/regression.R

@@ -1,154 +0,0 @@
-#######################
-# REGRESSION ANALYSIS
-#######################
-
-###########
-# USAGE
-###########
-
-# Usage: echo <in_json> | Rscript regression.R > <out_json>
-
-#   in_json: [string] input data in JSON format. Streamed through stdin.
-#   out_json: [string] regression results in JSON format. Streamed to stdout.
-
-# Input JSON specifications:
-# {
-#   "regressionType": regression type (linear/logistic/cox)
-#   "binpath": server bin path
-#   "data": [{}] per-sample data values
-#   "outcome": {
-#     "id": variable id
-#     "name": variable name
-#     "rtype": type of R variable ("numeric", "factor")
-#     "timeToEvent": {} (only for cox outcome)
-#       "timeScale": time/age
-#       "timeId": id of time variable (for 'time' time scale)
-#       "agestartId": id of age start variable (for 'age' time scale)
-#       "ageendId": id of age end variable (for 'age' time scale)
-#       "eventId": id of event variable
-#     "categories": {} (only for logistic outcome)
-#       "ref": reference category of outcome
-#       "nonref": non-reference category of outcome
-#   }
-#   "independent": [
-#     {
-#       "id": variable id
-#       "name": variable name
-#       "type": type of independent variable ("snplst", "snplocus", "spline", "other")
-#       "rtype": type of R variable ("numeric", "factor")
-#       "refGrp": reference group
-#       "interactions": [] ids of interacting variables (optional)
-#       "spline": {} cubic spline settings (only for spline variable)
-#         "knots": [] knot values
-#         "plotfile": output png file of spline plot
-#     }
-#   ]
-# }
-#
-#
-# Output JSON specifications:
-# [{
-#   data: {
-#     "id": id of snplocus term (empty when no snplocus terms are present)
-#     "data": {
-#       "sampleSize": sample size of analysis,
-#       "eventCnt": number of events (only for cox regression),
-#       "residuals": { "header": [], "rows": [] },
-#       "coefficients": { "header": [], "rows": [] },
-#       "type3": { "header": [], "rows": [] },
-#       "totalSnpEffect": { "header": [], "rows": [] } (only for snplocus interactions),
-#       "tests": { "header": [], "rows": [] } (only for cox regression),
-#       "other": { "header": [], "rows": [] },
-#       "warnings": [] warning messages
-#     },
-#   }
-#   benchmark: {} benchmarking results
-# }]
-
-
-###########
-# CODE
-###########
-
-suppressPackageStartupMessages({
-  library(jsonlite)
-  library(survival)
-  library(parallel)
-  library(lmtest)
-})
-
-benchmark <- list()
-
-################
-# PREPARE DATA #
-################
-
-# stream in json input
-stime <- Sys.time()
-con <- file("stdin", "r")
-json <- readLines(con)
-close(con)
-input <- fromJSON(json)
-etime <- Sys.time()
-dtime <- etime - stime
-benchmark[["read_json_input"]] <- unbox(paste(round(as.numeric(dtime), 4), attr(dtime, "units")))
-
-# import regression utilities
-source(paste0(input$binpath, "/utils/regression.utils.R"))
-
-# prepare data table
-stime <- Sys.time()
-dat <- prepareDataTable(input$data, input$independent)
-etime <- Sys.time()
-dtime <- etime - stime
-benchmark[["prepareDataTable"]] <- unbox(paste(round(as.numeric(dtime), 4), attr(dtime, "units")))
-
-
-##################
-# BUILD FORMULAS #
-##################
-
-stime <- Sys.time()
-formulas <- buildFormulas(input$outcome, input$independent, input$includeUnivariate)
-etime <- Sys.time()
-dtime <- etime - stime
-benchmark[["buildFormulas"]] <- unbox(paste(round(as.numeric(dtime), 4), attr(dtime, "units")))
-
-
-#save.image("~/test.RData")
-#stop("stop here")
-
-##################
-# RUN REGRESSION #
-##################
-
-# run a separate regression analysis for each formula
-# run the analyses in parallel using multiple cores
-stime <- Sys.time()
-cores <- detectCores()
-if (is.na(cores)) stop("unable to detect number of cores")
-reg_results <- mclapply(X = formulas, FUN = runRegression, regtype = input$regressionType, dat = dat, outcome = input$outcome, cachedir = input$cachedir, mc.cores = cores)
-etime <- Sys.time()
-dtime <- etime - stime
-benchmark[["runRegression"]] <- unbox(paste(round(as.numeric(dtime), 4), attr(dtime, "units")))
-
-
-##################
-# PARSE RESULTS #
-##################
-
-if (isTRUE(input$includeUnivariate)) {
-  # univariate analysis included along with multivariable analysis
-  # parse the univariate/multivariable results
-  reg_results <- parseUniMultiResults(reg_results, input$regressionType)
-}
-
-out <- list(data = reg_results, benchmark = benchmark)
-
-
-##################
-# OUTPUT RESULTS #
-##################
-
-# Export results as json to stdout
-toJSON(out, digits = NA, na = "string")