nortimecoursematrix: Normalization with datasets of time-course metabolomic study.

Description Usage Arguments Examples

View source: R/norm_timecoursedata.R

Description

This function handles normalizing the time-course metabolomic data using 168 methods/strategies.

Usage

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nortimecoursematrix(
  datatype,
  fileNameC,
  IS,
  impt = 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).

fileNameC

Please find the detail information of the file format from those six sample files in the working directory (in github) “idrblab/METNOR/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.

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

NORMALIZATION METHODS1

nmal2

NORMALIZATION METHODS2

nmals

NORMALIZATION METHODS TIMESERIES

Examples

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

idrblab/NOREVA2020 documentation built on Sept. 14, 2020, 12:04 a.m.