Creates an object of class QFeatures from text file.

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 = "myDataset",
  sample,
  indQData,
  keyId = "AutoID",
  indexForMetacell = NULL,
  logData = FALSE,
  force.na = TRUE,
  typeDataset,
  parentProtId = NULL,
  analysis = "foo",
  description = NULL,
  processes = NULL,
  typePipeline = NULL,
  software = NULL,
  name = "original"
)

Arguments

data

The name of a tab-separated file that contains the data.

file

A 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)

indexForMetacell

They must be in the same order as the samples in the experimental design

logData

xxx

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.

description

A text which describes the 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

Samuel Wieczorek, Manon Gaudin

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)


qdata.indices <- 56:61
qdata.names <- colnames(data)[qdata.indices]


sample.file <- system.file("extdata", "samples_Exp1_R25.txt", package = "DaparToolshedData")

sample <- read.table(sample.file, header = TRUE, sep = " ", as.is = TRUE, stringsAsFactors = FALSE)


metacell.indices <- 43:48
metacell.names <- colnames(data)[metacell.indices]



ft <- createQFeatures(file = data.file,
  data = data, 
  sample = sample,
  indQData = 56:61,
  keyId = "Sequence",
  analysis = "test",
  logData = TRUE,
  indexForMetacell = as.numeric(43:48),
  typeDataset = "peptide",
  parentProtId = "Protein_group_IDs",
  force.na = TRUE,
  software = "maxquant"
  )
#> Checking arguments.
#> Loading data as a 'SummarizedExperiment' object.
#> Formatting sample annotations (colData).
#> Formatting data as a 'QFeatures' object.
#> Setting assay rownames.


ft <- createQFeatures(file = data.file,
  data = data, 
  sample = sample,
  indQData = 56:61,
  keyId = "Sequence",
  analysis = "test",
  logData = TRUE,
  typeDataset = "peptide",
  parentProtId = "Protein_group_IDs",
  force.na = TRUE,
  software = "maxquant"
)
#> Checking arguments.
#> Loading data as a 'SummarizedExperiment' object.
#> Formatting sample annotations (colData).
#> Formatting data as a 'QFeatures' object.
#> Setting assay rownames.




ft <- createQFeatures(file = data.file,
  data = data, 
  sample = sample,
  indQData = qdata.names,
  keyId = "Sequence",
  analysis = "test",
  indexForMetacell = metacell.names,
  typeDataset = "peptide",
  parentProtId = "Protein_group_IDs",
  force.na = TRUE,
  software = "maxquant")
#> Checking arguments.
#> Loading data as a 'SummarizedExperiment' object.
#> Formatting sample annotations (colData).
#> Formatting data as a 'QFeatures' object.
#> Setting assay rownames.