createQCreportObject: Create initial qcrepotobject structure from input variable

In computational-metabolomics/qcrms: Creates quality control output from XCMS output

Description

Create initial qcrepotobject structure from input variable

Usage

createQCreportObject(
  data_file,
  projectdir,
  author = "",
  metaData_file = NULL,
  raw_path = NULL,
  InternalProjectRef = "",
  Dataset = "",
  Organisation = "",
  QC_label = "QC",
  Blank_label = "Blank",
  classLabel = "Class",
  excludeQC = c(1L:5L),
  assay = NULL,
  plot_eic = TRUE,
  pca_scores_labels = "all",
  mv_filter_method = "across",
  mv_filter_frac = 0.5,
  xcms_output = "xset",
  msms_label = "MSMS",
  group_names = NULL
)

Arguments

data_file	Rdata file containing XCMS output, object should be called xset
projectdir	Folder where Rdata file is located and where output should be directed
author	Character sring woth reports author name, optional
metaData_file	Files in xlsx format containing sample names and class labels
raw_path	File path where mzML files are located
InternalProjectRef	Character string containing project reference, optional
Dataset	Character string to describe data set, optional
Organisation	Character string containing organisation name, optional
QC_label	Label used for QC samples
Blank_label	Label usef for QC samples
classLabel	Columns name in meta data file to use for class labels, default value is Class
excludeQC	Which QC samples to exclude from RSD% calculations, signal batch correction and PCA plots
assay	Names for analytical assay, if set to NULL name of the input Rdata file will be used
plot_eic	Will create pdf fail with selected peak EIC's if set to TRUE
pca_scores_labels	Defines if sample labels should be added to filtered data PCA scores plot
mv_filter_method	Defines what method for MV filter
mv_filter_frac	Threshod of faction of detection of MV filter
xcms_output	Name of the R object in Rdata file containing XCMS outputs
msms_label	Label used for MS/MS data files
group_names	character(), character vector containing uique sample group identifiers in the raw data files. If left empty function will attemp to fill in class labels for blank and QC samples.

computational-metabolomics/qcrms documentation built on Jan. 18, 2021, 1:46 a.m.