WISP.getPureCentro: WISP.getPureCentro
In cit-bioinfo/WISP: Weighted In Silico Pathology

Description Usage Arguments Value Author(s)

Get pure population centroid profiles.

WISP.getPureCentro(data,cl,pureSamples_filtering = TRUE, nb_markers_selection = c("custom", "optim_kappa")[1],   nb_markers_max_perClass = 50, markers_cutoff_pval_anovatest = 0.05, markers_pval_anovatest_fdr = TRUE, markers_cutoff_auc = 0.8, pureSamples_deltaTopWeights = 0.5, plot_heatmap = TRUE, add_markers = NULL, col_purePop = NULL, sum_LessThanOne = TRUE)

`data`	data.frame of gene expression restricted to samples considered as pure by the user.
`cl`	vector of pure population class for each sample, where samples are in the same order than in data object. vector names must refer to sample names.
`pureSamples_filtering`	should WISP proceeds its pure sample filtering
`nb_markers_selection`	marker selection method: custom means based on nb_markers_max_perClass, optim_kappa will find the optimal number of markers based on the conditional number.
`nb_markers_max_perClass`	maximum number of markers per class (pure polulations).
`markers_cutoff_pval_anovatest`	cutoff used to retrieve significant genes based on the ANOVA test comparing the different pure populations.
`markers_pval_anovatest_fdr`	should fdr adjusted P-value be used to test gene significance?
`markers_cutoff_auc`	cutoff used for AUC criteria in the marker selection procedure if nb_markers_selection = custom
`pureSamples_deltaTopWeights`	weight difference between the 2 highest weights for a sample.
`plot_heatmap`	whether display heatmap of kept and removed sample expression profiles based on final marker selection.
`add_markers`	(optional) vector of gene names to be added in the centroid signature.
`col_purePop`	(optional) vector of colors for the pure populations. vector names must refer to pure population names.
`sum_LessThanOne`	sum of coefficients less that one (TRUE) or equal to one (FALSE).

The ouput is a list with following objects:

`genescentro`	centroids of pure populations based on the pure samples.
`indkept`	pure samples kept by the procedure.
`indremoved`	samples not considered as pure that where removed by WISP.
`genesclasses`	list of markers that were used in centroid calculation for each pure populations.