preprocess DIANN ouput, filter by q_value and nr_peptides

Description

preprocess DIANN ouput, filter by q_value and nr_peptides

Usage

preprocess_DIANN(
  quant_data,
  fasta_file,
  annotation,
  pattern_contaminants = "^zz|^CON|Cont_",
  pattern_decoys = "^REV_|^rev",
  q_value = 0.01,
  hierarchy_depth = 1,
  nr_peptides = 1
)

Arguments

quant_data	path to quantification data file
fasta_file	path to fasta file(s)
annotation	annotation list from read_annotation
pattern_contaminants	regex pattern for contaminants
pattern_decoys	regex pattern for decoys
q_value	q-value threshold for filtering
hierarchy_depth	hierarchy depth for aggregation
nr_peptides	minimum number of peptides per protein

Value

list with lfqdata and protein annotation

Examples

library("prolfquapp")

x <- get_DIANN_files("inst/application/DIANN/2706527/")

annotation <- file.path("inst/application/DIANN/2706527/dataset.csv") |>
  readr::read_csv() |>
  prolfquapp::read_annotation(QC = TRUE)
x$fasta
undebug(preprocess_DIANN)
xd <- preprocess_DIANN(x$data, x$fasta, annotation)
xd$lfqdata$hierarchy_counts()
xd <- preprocess_DIANN(x$data, x$fasta, annotation, nr_peptides = 2)
xd$lfqdata$hierarchy_counts()