make_benchmark: make Benchmark

In wolski/prolfqua: Proteomics Label Free Quantification

make Benchmark

Description

make Benchmark

Usage

make_benchmark(
  prpr,
  contrast = "contrast",
  toscale = c("p.value"),
  avgInt = "avgInt",
  fcestimate = "diff",
  benchmark = list(list(score = "diff", desc = TRUE), list(score = "statistic", desc =
    TRUE), list(score = "scaled.p.value", desc = TRUE)),
  FDRvsFDP = list(list(score = "FDR", desc = FALSE)),
  model_description = "protein level measurments, linear model",
  model_name = "prot_med_lm",
  hierarchy = c("protein_Id"),
  summarizeNA = "statistic"
)

Arguments

prpr	prepared data, e.g. function ionstar_bench_preprocess
contrast	column with names of the contrast
toscale	which scores to scale using fcestimate, typically p.value
avgInt	column with average intensity
fcestimate	column with FC estimate
benchmark	which scores to benchmark e.g. diff, statistics
FDRvsFDP	which score to plot against the false discovery proportion
model_description	string describing the model
model_name	name of the model, compatible with make.names output.
hierarchy	name of column with protein ID.
summarizeNA	summarizeNA

Value

Benchmark

See Also

Other benchmarking: Benchmark, INTERNAL_FUNCTIONS_BY_FAMILY, ionstar_bench_preprocess(), ms_bench_add_scores(), ms_bench_auc()

wolski/prolfqua documentation built on Oct. 31, 2024, 9:22 a.m.