Description Usage Arguments Details Value Author(s) Examples

Given a `data.frame`

or
`matrix`

containing xy coordinates, it returns the slope and distance from
origin of each coordinate.

1 |

`array` |
A |

`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 |

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.

A matrix (ncol=3) containing

1 2 3 | ```
slope
angle (in degrees)
distance from origin
``` |

of each x,y coordinates in a matrix.

Aedin Culhane

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ```
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)
``` |

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