BuildSummary: Gets the Predicted Dosage from Combined Dosage Calls

In dsherma7/PolyploidDosageCalling: Calls the Dosage From Tetraploid qPCR Data (CT/RQ Values)

Description

Checks the different models' accuracy against the controls and then sets the predicted values to be the best model.

Usage

BuildSummary(Job, NotDone, PlateSz = 84, assays = c("Assay3", "Assay2", "Assay1",
  "Assay3#", "Assay1#"),
  dose.dir = "/path/to/data",
  Summary.File = paste0(dose.dir, "../summary/20", substr(Job, 2, 3),
  "_ProductionSummary.csv"), header = c("RecId", "Job", "#Samples", "Name",
  "Clone-plant_ID", "Entry", "TissID", "Clone ID", "Rack", "RackOrder",
  "Well Position", "DNA Well", "Pedigree", "Pedigree Long",
  c(matrix(sapply(assays[-grep("#", assays)], function(x) {     c(paste0("(", x,
  ")", c(" PCR", " RackOrder", " PCR Well", " A1 dRn", " A2 dRn")), paste0(x,
  c("", "_Pr", "_QC"))) }), nrow = 1)), c(matrix(sapply(assays[grep("#",
  assays)], function(x) c(paste0("(", x, ")", c(" PCR", " RackOrder",
  " PCR Well", " CT", " CT PEF", " dCT", " RQ")), paste0(x, c("", "_Pr",
  "_QC")))), nrow = 1), "Action", "uid")), num.cols = c("CT", "CT.PEF", "dCT",
  "RQ", "Allele1.Delta.Rn", "Allele2.Delta.Rn", matrix(rbind(assays,
  paste0(assays, "_Pr")), nrow = 1), paste0(assays, "_QC")),
  Assay.Cols = c("PCR", "RackOrder", "PCR Well", "A1 dRn", "A2 dRn", "CT",
  "CT PEF", "dCT", "RQ"),
  consol.cols.num = c(c(matrix(sapply(assays[-grep("#", assays)], function(x)
  {     c(paste0("(", x, ")", c(" A1 dRn", " A2 dRn")), paste0(x, c("", "_Pr")))
  }), nrow = 1)), c(matrix(sapply(assays[grep("#", assays)], function(x)
  c(paste0("(", x, ")", c(" CT", " CT PEF", " dCT", " RQ")), paste0(x, c("",
  "_Pr")))), nrow = 1))),
  consol.cols.str = c(c(matrix(sapply(assays[-grep("#", assays)], function(x)
  {     c(paste0("(", x, ")", c(" PCR", " RackOrder", " PCR Well"))) }), nrow =
  1)), c(matrix(sapply(assays[grep("#", assays)], function(x) c(paste0("(", x,
  ")", c(" PCR", " RackOrder", " PCR Well")))), nrow = 1))))

Arguments

Job	Name of the current job.
NotDone	Which PCR plates of the current job have yet to be added to the summary?
PlateSz	Size of the DNA plates excluding controls. For example, a 96 well DNA plate with 12 controls would have PlateSz = 84. Used to index the output.
assays	List of all possible assays. Default = c('Assay3','Assay2','Assay1','Assay3#','Assay1#')
dose.dir	Directory of where to find the Dosage.csv files. Should have sub-directory structure of dose.dir/<Job>/<PCR>.Dosage.csv
Summary.File	Name of the current summary file

dsherma7/PolyploidDosageCalling documentation built on May 23, 2019, 6:06 p.m.