prepareData: Wrapper function to transform data for statistical analysis

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

Description

Wrapper function to transform data for statistical analysis

Usage

prepareData(
  Data,
  classes,
  blank = "BLANK",
  PQN = FALSE,
  mv_impute = TRUE,
  glogScaling = TRUE,
  qc_label = "QC",
  ignorelabel = "Removed",
  checkNA = TRUE,
  store_lambda = FALSE
)

Arguments

Data	Data frame.
classes	Vector of class labels.
blank	Label used for blank samples, if set to NULL no samples will be removed.
PQN	Can be set to T or F, to perform PQN normalisation.
mv_impute	T or F, indicates if missing value imputation has to be carried.
glogScaling	T or F, applie glog transformation to the given data.
qc_label	Label used for QC samples. If set to NULL, assumes that no QC samples are present in data set.
ignorelabel	Label for samples which should be excluded from processed data.
checkNA	removes rows or columns containing all NA's, also will chek if only all QC or analytical samples contain missing values.
store_lambda	If value of glog optimised lambda parameter needs to be returned.

Value

List of processed data table and RSD

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