writeHtmlResTestsByAnnot: Tests if groups of samples are differently distributed on the...
In MineICA: Analysis of an ICA decomposition obtained on genomics data

Description Usage Arguments Details Value Author(s) See Also

View source: R/functions_comp2annottests.R

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".

  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)

`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)`.

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.

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

Anne Biton

p.adjust, qualVarAnalysis, quantVarAnalysis

MineICA documentation built on Nov. 8, 2020, 5:35 p.m.