sumstats {made4} | R Documentation

## Summary statistics on xy co-ordinates, returns the slopes and distance from origin of each co-ordinate.

### Description

Given a `data.frame` or `matrix` containing xy coordinates, it returns the slope and distance from origin of each coordinate.

### Usage

    sumstats(array, xax = 1, yax = 2)

### Arguments

`array` | A `data.frame` or `matrix` containing xy coordinates, normally a \$co, \$li from `dudi` such as PCA or COA, or \$ls from `bga`
`xax` | Numeric, an integer indicating the column of the x axis coordinates. Default xax=1
`yax` | Numeric, an integer indicating the column of the x axis coordinates. Default xax=2

### Details

In PCA or COA, the variables (upregulated genes) that are most associated with a case (microarray sample), are those that are projected in the same direction from the origin.

Variables or cases that have a greater contribution to the variance in the data are projected further from the origin in PCA. Equally variables and cases with the strong association have a high chi-square value, and are projected with greater distance from the origin in COA, See a description from Culhane et al., 2002 for more details.

Although the projection of co-ordinates are best visualised on an xy plot, `sumstats` returns the slope and distance from origin of each x,y coordinate in a matrix.

### Value

A matrix (ncol=3) containing

       slope
       angle (in degrees)
       distance from origin

of each x,y coordinates in a matrix.

### Author(s)

Aedin Culhane

### Examples

    data(khan)

    if (require(ade4, quiet = TRUE)) {

    khan.bga<-bga(khan$train, khan$train.classes)}

    plotarrays(khan.bga$bet$ls, classvec=khan$train.classes)
    st.out<-sumstats(khan.bga$bet$ls)

    # Get stats on classes  EWS and BL
    EWS<-khan$train.classes==levels(khan$train.classes)[1]
    st.out[EWS,]

    BL<-khan$train.classes==levels(khan$train.classes)[2]
    st.out[BL,]

    # Add dashed line to plot to highlight min and max slopes of class BL
    slope.BL.min<-min(st.out[BL,1])
    slope.BL.max<-max(st.out[BL,1])
    abline(c(0,slope.BL.min), col="red", lty=5)
    abline(c(0,slope.BL.max), col="red", lty=5)

[Package made4 version 1.66.0 Index]