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Run the pure-R SAINTexpress engine

Source: R/run_saint.R
run_saint.Rd

Dispatches to the spectral-count or intensity scorer.

Usage

run_saint(si, mode = c("spc", "int"), optimizer = c("base", "nloptr"), ...)

Arguments

si

A named list with elements inter, prey, bait (data frames).

mode

"spc" for spectral counts, "int" for intensities.

optimizer

"base" (default; uses stats::optim()) or "nloptr" (uses NLopt COBYLA via the optional nloptr package).

...

Additional arguments forwarded to the internal scorers saint_spc_r() or saint_int_r() (e.g. R, L, frequency, p2p_mapping).

Value

A data frame in the SAINTexpress list.txt shape.

Examples

si <- list(
  inter = data.frame(
    ipId = c("IP1", "IP1", "IP2", "IP2", "IP3", "IP4"),
    baitId = c("BaitA", "BaitA", "BaitA", "BaitA", "Ctrl", "Ctrl"),
    preyId = c("Prey1", "Prey2", "Prey1", "Prey2", "Prey1", "Prey2"),
    quant = c(20, 1, 18, 1, 1, 1)
  ),
  prey = data.frame(
    preyId = c("Prey1", "Prey2"),
    preyLength = c(500, 500),
    preyGeneId = c("Gene1", "Gene2")
  ),
  bait = data.frame(
    ipId = c("IP1", "IP2", "IP3", "IP4"),
    baitId = c("BaitA", "BaitA", "Ctrl", "Ctrl"),
    CorT = c("T", "T", "C", "C")
  )
)
run_saint(si, mode = "spc")
#>    Bait  Prey PreyGene  Spec SpecSum AvgSpec NumReplicates ctrlCounts AvgP MaxP
#> 1 BaitA Prey1    Gene1 20|18      38      19             2        1|0    1    1
#> 2 BaitA Prey2    Gene2   1|1       2       1             2        0|1    0    0
#>   TopoAvgP TopoMaxP SaintScore logOddsScore FoldChange BFDR boosted_by
#> 1        1        1          1        24.22         38    0           
#> 2        0        0          0        -0.19          2    0