In lgatto/synapter: Label-free data analysis pipeline for optimal identification and quantitation

knitr::read_chunk(system.file("reports", "scripts", "synergise.R",
                              package="synapter"))

Input {.tabset}

Files

inputFiles <-
    rbind(c("Identification peptide:", basename(obj$IdentPeptideFile), nrow(obj$IdentPeptideData)),
          c("Quantitation peptide:",   basename(obj$QuantPeptideFile), nrow(obj$QuantPeptideData)),
          c("Quantitation Pep3D:",     basename(obj$QuantPep3DFile),   nrow(obj$QuantPep3DData)),
          c("Fasta file:",    basename(obj$DbFastaFile), ""))
colnames(inputFiles) <- c("", "File name", "Number of features")
knitr::kable(inputFiles, align="llr")

General Parameters

parameters <-
    rbind(c("Master", master),
          c("Peptide FDR", fdr),
          c("Protein FPR", fpr),
          c("Peptide Length", peplen),
          c("Missed cleavages", missedCleavages),
          c("Isoleucin equals Leucin", IisL),
          c("Identification mass tolerance (ppm)", identppm),
          c("Quantitation mass tolerance (ppm)", quantppm),
          c("Loess span (RT modelling)", span.rt),
          c("Filtering unique peptides", as.character(uniquepep)))
colnames(parameters) <- c("Parameter name", "Value")
knitr::kable(parameters, align="lr")

Grid Search Parameters

gridParameters <-
    rbind(c("Mass tolerance (ppm) start", grid.ppm.from),
          c("Mass tolerance (ppm) end", grid.ppm.to),
          c("Mass tolerance (ppm) by", grid.ppm.by),
          c("Retention time stdev start", grid.nsd.from),
          c("Retention time stdev end", grid.nsd.to),
          c("Retention time stdev by", grid.nsd.by),
          c("Feature proportion ", grid.subset),
          c("Number of features", grid.n),
          c("parameters selection", grid.param.sel))
colnames(gridParameters) <- c("Grid parameter", "Value")
knitr::kable(gridParameters, align="lr")

Filtering

Peptide False Discovery Rate

Peptide Scores

Peptide Numbers

Peptide FDR

Mass tolerance

Retention Time Modelling

Retention Time Model

Feature Space

plotFeatures(obj, what="all")

Grid Optimisation

r if(grid.n) { paste0("Using", grid.n, "features.") } else { paste0("Using ", grid.subset * 100, "% of the data.") }

# abuse inline r here to show the progress bar of the gridsearch in the
# R console - regular r chunks capture stdout

r if (grid.n) { searchGrid(obj, ppms=seq(grid.ppm.from, grid.ppm.to, grid.ppm.by), nsds=seq(grid.nsd.from, grid.nsd.to, grid.nsd.by), imdiffs=Inf, n=grid.n, verbose=verbose) } else { searchGrid(obj, ppms=seq(grid.ppm.from, grid.ppm.to, grid.ppm.by), nsds=seq(grid.nsd.from, grid.nsd.to, grid.nsd.by), imdiffs=Inf, subset=grid.subset, verbose=verbose) }

plotGrid(obj, what="details")

Grid Tables {.tabset}

names <- c("total", "model", "details")
what <- c("total", "model", "details")
for (i in seq(along=names)){
  cat("\n####", names[i], "\n")
  cat("\n##### Image\n")
  plotGrid(obj, what=what[i])
  cat("\n\n##### Table\n")
  print(knitr::kable(as.data.frame(getGrid(obj)[[i]][,,1])))
  cat("\nBest Grid Value ", names[i], ": ", getBestGridValue(obj)[i], "\n", sep="")
  #cat("\n##### Best Grid Parameters\n")
  print(knitr::kable(as.data.frame(getBestGridParams(obj)[[i]])))
}

Grid Details

gridDetails <- do.call(rbind, getGridDetails(obj))
cond <- do.call(rbind, strsplit(rownames(gridDetails), ":"))[, 1:2] ## imdiff not supported by synergise1
colnames(cond) <- c("nsd", "ppm")
gridDetails <- cbind(cond, gridDetails)
gridDetails[] <- as.numeric(gridDetails)
rownames(gridDetails) <- NULL
knitr::kable(as.data.frame(gridDetails))

Best Grid Parameters

Setting best grid parameters using 'r grid.param.sel'

• Mass tolerance (ppm): r obj$PpmError
• Number of retention time stdev: r obj$RtNsd

EMRT Matching

findEMRTs(obj)
rescueEMRTs(obj, mergedEMRTs)
plotEMRTtable(obj)

Performance

Enrichment

Overlap

Source

Exported Files

• Identification Peptides
• Quantitation Peptides
• Merged Peptides
• Matched Peptides
• QuantPeptides.csv
• Grid Details
• Saved R Object (binary)

Full Analysis Log

Session Info

lgatto/synapter documentation built on Sept. 28, 2022, 6:53 a.m.