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make Benchmark

Source: R/Benchmark.R
make_benchmark.Rd

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()