get_iBAQ: get_iBAQ

In mgerault/DIAgui: A shiny app for processing DIAnn output in proteomics

get_iBAQ

Description

Function to calculate iBAQ quantities from a dataset.

Usage

get_iBAQ(
  dataset,
  proteinDB = list(),
  id_name = "Protein.Group",
  ecol = 5:7,
  peptideLength = c(5, 36),
  nbMiscleavages = 0,
  proteaseRegExp = getProtease("trypsin"),
  log2_transformed = TRUE,
  keep_original = TRUE
)

Arguments

dataset	A data frame that you want to get the iBAQ quantities from.
proteinDB	A list that contains for each protein the theoretical peptide sequence. It doesn't have to be the same length as the number of proteins from the dataset; if it's the case, value from proteins that are not in this list will be set to NA.
id_name	The name of the column that contains the protein IDs.
ecol	The indexes of the intensity columns.
peptideLength	A vector that contains the minimum and maximum peptide length.
nbMiscleavages	The number of miss cleavages.
proteaseRegExp	The enzyme you used to digest proteins.
log2_transformed	Logical to tell if you want to log2 transformed the data.
keep_original	Logical to tell if you want to keep the original intensity values.

Details

This function use three function from SafeQuant package from github eahrne/SafeQuant. Those three function are simple and small, so to facilitate dependencies and lower the size of this package, I chose to copy-paste those three.

Erik Ahrne (2021). SafeQuant: A Toolbox for the Analysis of Proteomics Data. R package version 2.3.4.

Value

The dataset with the iBAQ quantities and number of theoretical peptides.

Examples

library(DIAgui)
data <- small_report %>% dplyr::filter(Q.Value <= 0.01 & PG.Q.Value <= 0.01)
data <- diann_maxlfq(data,
                  group.header="Protein.Group",
                  id.header = "Precursor.Id",
                  quantity.header = "Precursor.Normalised"
                  )
nc <- ncol(data)
data$Protein.Group <- rownames(data)
rownames(data) <- 1:nrow(data)
data <- data[order(data$Protein.Group),]
data <- data[,c((nc+1):ncol(data), 1:nc)]
sequence_list <- getallseq(pr_id = data$Protein.Group)
iBAQ <- get_iBAQ(data, sequence_list, ecol = 2:4)

mgerault/DIAgui documentation built on Nov. 7, 2024, 12:12 a.m.