MIGSAres-GoAnalysis: Explore Gene Ontology gene sets in MIGSAres

In MIGSA: Massive and Integrative Gene Set Analysis

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)

MIGSA documentation built on Nov. 8, 2020, 8:26 p.m.