BuildMetaCell: Builds cells metadata

In prostarproteomics/DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

Builds cells metadata

Description

This function the cells metadata info base on the origin of identification for entities. There are actually two different type of origin which are managed by DAPAR: - "Maxquant-like" info which is represented by strings/tags, - Proline-like where the info which is used is an integer

Usage

BuildMetaCell(from, level, qdata = NULL, conds = NULL, df = NULL)

Arguments

from	A string which is the name of the software from which the data are. Available values are 'maxquant', 'proline' and 'DIA-NN'
level	xxx
qdata	An object of class MSnSet
conds	xxx
df	A list of integer xxxxxxx

Value

xxxxx

Author(s)

Samuel Wieczorek

Examples

file <- system.file("extdata", "Exp1_R25_pept.txt", package = "DAPARdata")
data <- read.table(file, header = TRUE, sep = "\t", stringsAsFactors = FALSE)
metadataFile <- system.file("extdata", "samples_Exp1_R25.txt",
    package = "DAPARdata")
metadata <- read.table(metadataFile,
    header = TRUE, sep = "\t", as.is = TRUE,
    stringsAsFactors = FALSE)
conds <- metadata$Condition
qdata <- data[, seq.int(from = 56, to = 61)]
df <- data[, seq.int(from = 43, to = 48)]
df <- BuildMetaCell(
    from = "maxquant", level = "peptide", qdata = qdata,
    conds = conds, df = df)
df <- BuildMetaCell(
    from = "proline", level = "peptide", qdata = qdata,
    conds = conds, df = df)

prostarproteomics/DAPAR documentation built on March 28, 2024, 4:44 a.m.