statAnalysis provide the statistical analysis for metabolomics data or others.

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Description

statAnalysis provide the statistical analysis for metabolomics data or others.

Usage

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statAnalysis(file, Frule = 0.8, imputeM = "KNN", glog = TRUE,
  test.multi = TRUE, nvarRF = 10, scaling = "Pareto", silt = 500,
  pcax = 1, pcay = 2)

Arguments

file

a file with the expression information.

Frule

The cut-off value for missing value filter function.

imputeM

The parameter for imputation method.(i.e., nearest neighbor averaging, "KNN"; minimum values for imputed variables, "min", median values for imputed variables (Group dependent) "median").

glog

is a data index for log transformation, with the default value TRUE.

test.multi

must be an index for statistic analysis, with the default value TRUE.

nvarRF

shows the number of variables in Gini plot of Randomforest model (=< 100).

scaling

is index of scaling method index for statistic analysis (PCA or PLS-DA). 'pareto', 'Pareto', 'p' or 'P' can be used for specifying the Pareto scaling. 'auto', 'Auto', 'auto', 'a' or 'A' can be used for specifying the Auto scaling (or unit variance scaling). 'vast', 'Vast', 'v' or 'V' can be used for specifying the vast scaling. 'range', 'Range', 'r' or 'R' can be used for specifying the Range scaling.

silt

shows the number of permutation times

pcax

shows principal components in PCA model for the x-axis.

pcay

shows principal components in PCA model for the y-axis.