MIGSAres-GOanalysis {MIGSA} | R Documentation

## Explore Gene Ontology gene sets in MIGSAres

### Description

`migsaGoTree` plots the GO tree/s present in migsaRes. `getHeights` returns the heights of given a list of ids (GO IDs).

### Usage

    `MIGSAres-GOanalysis`(migsaRes)

    migsaGoTree(migsaRes, ...)

    ## S4 method for signature 'MIGSAres'
    migsaGoTree(
      migsaRes,
      categories = rep(NA, ncol(migsaRes) - 3),
      categColors = "red",
      ont = "BP",
      legendPos = "topleft"
    )

    goTree(treeInfo, ...)

    ## S4 method for signature 'data.frame'
    goTree(treeInfo, ont = "BP", legends = NA, legendPos = "topleft")

    getHeights(ids, ...)

    ## S4 method for signature 'character'
    getHeights(ids, minHeight = TRUE)

### Arguments

`migsaRes` | MIGSAres object. It must contain at least one GO gene set.
`...` | not in use.
`categories` | vector. Each experiment category, it will print different node color for each. Can have NAs. Must have length equal to number of experiments, i.e. length(categories) == ncol(migsaRes)-3
`categColors` | character. Color for each category. Must have the same length as the number of different categories.
`ont` | character. One of "BP", "CC" or "MF". Selected ontology to plot.
`legendPos` | . Parameter passed to legend function.
`treeInfo` | . Data.frame with GO ids as rownames, and three columns: Enriched (logical), Important (logical) and Color (character). If Enriched is true then it will be ploted, if Important is true then it will have another shape, Color has the color name to use.
`legends` | . Matrix with two columns, each col is a pair (lengend, color).
`ids` | character vector indicating the queried GO ids.
`minHeight` | logical indicating if the minimum or maximum height must be calculated. If it is FALSE then the longest path to the root is calculated, otherwise, the shortest path.

### Value

If migsaGoTree: A list with the used data to plot. If getHeights: A list with each term height.

### Examples

    ## Lets load breast cancer results.
    data(bcMigsaRes)
    ###### migsaGoTree
    ## Get the first 40 Gene Ontology gene sets results from CC.
    goRes <- bcMigsaRes[bcMigsaRes$GS_Name == "CC", ]
    fst40goRes <- goRes[1:40, ]
    ## And lets plot the results GO trees.
    ## Not run:
    aux <- migsaGoTree(fst40goRes, ont = "CC")

    ## End(Not run)

    ###### getHeights
    ## Get the first 40 Gene Ontology gene sets IDs.
    goIds <- bcMigsaRes[bcMigsaRes$GS_Name %in% c("BP", "CC", "MF"), "id"]
    fst40goIds <- goIds[1:40, ]
    ## Not run:
    ## And lets get the heights in the GO tree structure.
    getHeights(fst40goIds)

    ## End(Not run)

[Package MIGSA version 1.12.0 Index]