preprocess_bgs – prolfquapp

preprocess DIANN ouput, filter by q_value and nr_peptides

Description

preprocess DIANN ouput, filter by q_value and nr_peptides

Usage

preprocess_BGS(
  quant_data,
  fasta_file,
  annotation,
  pattern_contaminants = "^zz|^CON|Cont_",
  pattern_decoys = "^REV_|^rev",
  q_value = 0.01,
  hierarchy_depth = 2,
  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 distinct (stripped) peptides per protein (>= 1, default 1)

Value

list with lfqdata and protein annotation

Examples

library("prolfquapp")

x <- get_BGS_files("DefaultParsing")
bgs <- read_BGS(x$data)
annot <- data.frame(raw.file = bgs$R.FileName |> unique(),
 Name = paste(c(rep("A",3),rep("B",3)),1:6, sep="_"),
group = c(rep("A",3),rep("B",3)))
annotation <- annot |> prolfquapp::read_annotation(QC = TRUE)
#debug(preprocess_BGS)
xd <- preprocess_BGS(x$data, x$fasta, annotation)