writeHtmlResTestsByAnnot: Tests if groups of samples are differently distributed on the...

In bitona/MineICA: Analysis of an ICA decomposition obtained on genomics data

Tests if groups of samples are differently distributed on the components according and do the corresponding plots.

Description

This internal function creates an HTML file containing a table of dimensions 'variables x components' with p-values. When a p-value is considered as significant according to the threshold cutoff, it is written in bold and filled with a link pointing to the corresponding plot. These plots are contained in images located in the path pathplot. To be identified by the function, the file syntax of each image file must be "index-of-component_colAnnot.typeImage".

Usage

  writeHtmlResTestsByAnnot(params, icaSet, res, res2,
    nameres = "p", nameres2 = "cor", onlySign = TRUE,
    cutoff = params["pvalCutoff"],
    cutoffDir = c("<=", ">="), path, pathplot = "plots/",
    filename = NULL, typeImage = "png", caption = "",
    keepVar)

Arguments

params	An object of class MineICAParams containing the parameters of the analysis
icaSet	An object of class IcaSet
res	A matrix or data.frame of dimension 'components x variables' containing numeric values that quantify the association of the components with sample variables (e.g p-values, FDR, correlation values). This is the matrix used to select the significant results according to cutoff and cutoffDir.
res2	A matrix or data.frame of dimension 'components x variables' containing numeric values that quantify the association of the components with sample annotations (e.g p-values, FDR, correlation values). It is only used as an additional result displayed in the output.
nameres	Name of the values contained in res, default is "p"
nameres2	Name of the values contained in res2, default is "cor"
onlySign	If TRUE (default), only the significant results are plotted
cutoff	The threshold p-value for statistical significance
path	A directory for the HTML file containing the p-value results
pathplot	A directory for the plots
filename	The name of the file where the results will be displayed in format HTML, if NULL no file is created
typeImage	The type of image file where each plot is saved
caption	The title of the HTML table
cutoffDir	The direction to be used with the cutoff: "inf" for "<=" and "sup" for ">="
keepVar	The variable labels to be considered, i.e a subset of the variables of icaSet available in varLabels(icaSet).

Details

If argument onlySign is TRUE, then only links to plots that are significant according to the given threshold are provided.

When res2 is not missing, the values contained in res2 are pasted to the values contained in res in the output array. nameres and nameres2 are used such as every element in the ouput array contains two indexed values: nameres=x, nameres2=y.

Value

Returns a data.frame of dimensions 'components x variables' containing the p-values of the non-parametric tests (Wilcoxon or Kruskal-Wallis tests) wich test if the samples groups defined by each variable are differently distributed on the components

Author(s)

Anne Biton

See Also

p.adjust, qualVarAnalysis, quantVarAnalysis

bitona/MineICA documentation built on April 23, 2023, 1:41 p.m.