Add protein lengths from fasta file to data frame (id_col - protein id column.)

Executes SAINTexpress on prepared input data. Delegates to the saintexpressbin package for the native binary / Docker engine, and to the saintexpress package for the pure-R engine. If `engine = "binary"` is requested but saintexpressbin is not installed, a warning is issued and the call falls back to the R engine.

Usage

add_protein_lengths(intdata, fasta, id_col = "protein_Id")

protein_2localSaint(
  xx,
  quantcolumn = "mq.protein.intensity",
  proteinID = "protein_Id",
  geneNames = proteinID,
  proteinLength = "protein.length",
  IP_name = "raw.file",
  baitCol = "bait",
  CorTCol = "CorT"
)

runSaint(
  si,
  filedir = getwd(),
  spc = TRUE,
  CLEANUP = TRUE,
  use_docker = NULL,
  engine = c("binary", "r"),
  optimizer = c("base", "nloptr")
)

Arguments

intdata

data.frame

fasta

list of sequences created with read.fasta

id_col

column with protein ids/accessions.

xx

data.frame in long format

quantcolumn

intensity column

proteinID

protein accession

geneNames

column with gene names

proteinLength

column with protein lengths

IP_name

raw.file

baitCol

column with bait definition (condition)

CorTCol

is it control or TRUE (SaintExpress speach)

si

output of protein_2localSaint function

filedir

where to store the saint express inputs

spc

if TRUE spectral counts, if FALSE intensities (see SAINTexpress documentation)

CLEANUP

TRUE remove all files generated by SAINTexpress

use_docker

logical or NULL. NULL (default) uses a native executable when available and falls back to Docker on macOS. TRUE forces Docker. FALSE forces native execution.

engine

execution engine. "binary" runs bundled SAINTexpress via saintexpressbin; "r" runs the R implementation via saintexpress.

optimizer

optimizer for engine = "r". "base" uses optim; "nloptr" uses NLopt COBYLA when nloptr is installed.

Value

`intdata` with an added `protein.length` column.

named list with `inter`, `prey`, and `bait` SAINT input tables.

list with SAINTexpress `listFile`, parsed `list`, and run `out`.

Examples

add_protein_lengths(
  data.frame(protein_Id = "P1"),
  list(P1 = "MPEPTIDE")
)
#>   protein_Id protein.length
#> 1         P1              8


bb <- prolfqua::prolfqua_data('data_IonstarProtein_subsetNorm')
bb$config <- bb$config$clone(deep = TRUE)
xx <- prolfqua::LFQData$new(bb$data, bb$config)
exampleDat <- xx$data_long() |>
  dplyr::mutate(CorT = dplyr::case_when(dilution. == "a" ~ "C", TRUE ~ "T"))
# sample protein lengths

tmp <- data.frame(protein_Id = unique(exampleDat$protein_Id))
tmp$proteinLength <- as.integer(runif(nrow(tmp), min = 150, max = 2500))
exampleDat <- dplyr::inner_join(tmp, exampleDat)
#> Joining with `by = join_by(protein_Id)`
res <- protein_2localSaint(exampleDat,quantcolumn = "medpolish",
                   proteinID = "protein_Id",
                   proteinLength = "proteinLength",
                   IP_name = "raw.file",
                   baitCol = "dilution.",
                   CorTCol = "CorT"
                   )

stopifnot(names(res) == c( "inter", "prey",  "bait"))