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
)

preprocess_BGS(
  quant_data,
  fasta_file,
  annotation,
  pattern_contaminants = "^zz|^CON|Cont_",
  pattern_decoys = "^REV_|^rev",
  q_value = 0.01,
  hierarchy_depth = 2
)

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

Value

list with lfqdata and protein annotation

Examples

if (FALSE) { # \dontrun{
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)
} # }
if (FALSE) { # \dontrun{
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)
} # }