nortimecoursematrix: Process the dataset of time-course metabolomic study.

In idrblab/NOREVA: R Package for Systematic Optimization of Metabolomic Data Processing

Process the dataset of time-course metabolomic study.

Description

based on a particular processing workflow (especially the one identified as well-performing for the studied metabolomic time-course dataset), this function outputs the resulting levels of all metabolites among all samples after the data processing based on that workflow.

Usage

nortimecoursematrix(
  datatype,
  fileName,
  IS,
  impt = NULL,
  qcsn = NULL,
  trsf = NULL,
  nmal = NULL,
  nmal2 = NULL,
  nmals = NULL
)

Arguments

datatype	Input the number of data type. If set 1, the dataset of time-course metabolomic study without QCSs and ISs. If set 2, the dataset of time-course metabolomic study with quality control samples (QCSs). If set 3, the dataset of time-course metabolomic study with dataset with internal standards (ISs).
fileName	Please find the detail information of the file format from those six sample files in the working directory (in github) “idrblab/NOREVA/data”
IS	Input the Column of Internal Standards. For example, the replacement of IS to 2,6,9,n indicates that the metabolites in the 2st, 6th, 9th, and nth columns of in your input dataset Input-Dataset.csv should be considered as the ISs or quality control metabolites. If there is only one IS, the column number of this IS should be listed If there are multiple ISs, the column number of all ISs should be listed and separated by comma (,)
impt	Input the name of imputation methods. If set 1, method of column mean imputation. If set 2, method of column median imputation. If set 3, method of half of the minimum positive value. If set 4, method of KNN imputation.
qcsn	Input the name of qc sample correction methods. If set 1, method of NWE (Nadaraya-Watson estimator). If set 2, method of LLR (local linear regression). If set 3, method of LPF (local polynomial fits).
trsf	Input the name of transformation methods. If set 1, method of cube root transformation. If set 2, method of log transformation. If set 3, none transformation method.
nmal	Allows the users to specify the NAME of the normalization method (default = null)
nmal2	Allows the users to specify the NAME of the normalization method (default = null)
nmals	Allows the users to specify the NAME of the IS-based normalization method (default = null)

Examples

nordata <- nortimecoursematrix(datatype = 1,
fileName = timec_non_data, impt = 1, trsf = 1, nmal = 1, nmal2 = 1)

idrblab/NOREVA documentation built on April 17, 2025, 2:04 p.m.