Usage
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.