import-export-QFeatures: Creates an object of class 'QFeatures' from text file.

In samWieczorek/Dapar2: Tools for the Differential Analysis of Proteins Abundance with R

Creates an object of class QFeatures from text file.

Description

Creates an object of class QFeatures from a single tabulated-like file for quantitative and meta-data and a dataframe for the samples description.

Usage

createQFeatures(
  data = NULL,
  file = NULL,
  sample,
  indQData,
  keyId = "AutoID",
  indQMetadata = NULL,
  force.na = TRUE,
  typeDataset,
  parentProtId = NULL,
  analysis = "foo",
  processes = NULL,
  typePipeline = NULL,
  software = NULL,
  name = "original"
)

Arguments

data	The name of a tab-separated file that contains the data.
file	character(1). The name of a file xxx
sample	A dataframe describing the samples (in lines).
indQData	A vector of string where each element is the name of a column in designTable that have to be integrated in the rowData() table of the QFeatures object.
keyId	A character(1) or numeric(1) which is the indice of the column containing the ID of entities (peptides or proteins)
indQMetadata	xxxxxxxxxxx
force.na	A boolean that indicates if the '0' and 'NaN' values of quantitative values must be replaced by 'NA' (Default is FALSE)
typeDataset	A string that indicates whether the dataset is about
parentProtId	A character(1) For peptide entities, a string which is the name of a column in rowData. It contains the id of parent proteins and is used to generate adjacency matrix and process to aggregation.
analysis	A character(1) which is the name of the MS study.
processes	A vector of A character() which contains the name of processes which has already been run on the data. Default is 'original'.
typePipeline	A character(1) The type of pipeline used with this dataset. The list of predefined pipelines in DaparToolshed can be obtained with the function pipelines(). Default value is NULL
software	A character(1)
name	A character(1) which is the name of the assay in the QFeatures object. Default is 'original'

Value

An instance of class QFeatures.

Author(s)

Samuel Wieczorek

Examples

{
data.file <- system.file("extdata", "Exp1_R25_pept.txt", package="DaparToolshedData")
data <- read.table(data.file, header=TRUE, sep="\t", as.is=TRUE, stringsAsFactors = FALSE)
sample.file <- system.file("extdata", "samples_Exp1_R25.txt", package="DaparToolshedData")
sample <- read.table(sample.file, header=TRUE, sep="\t", as.is=TRUE, stringsAsFactors = FALSE)
ft <- createQFeatures(data = data, sample = sample, indQData = 56:61, 
keyId = 'Sequence', analysis = 'test',
indQMetadata = 43:48, typeDataset = 'peptide',
parentProtId = 'Protein_group_IDs', forceNA = TRUE, software = 'maxquant')
}

samWieczorek/Dapar2 documentation built on May 13, 2022, 9:23 a.m.