Description Usage Arguments Details Value Examples

Calculates the x-coordinates for the PDF of a given pathway.

1 | ```
getXcoords(QSarray, path.index=1, addVIF=!is.null(QSarray$vif))
``` |

`QSarray` |
A QSarray object as output by qusage (or aggregateGeneSet) |

`path.index` |
either an integer between 1 and numPathways(QSarray), or the name of the pathway to retrieve. |

`addVIF` |
a logical indicating whether to use the VIF when calculating the variance |

The calculation of the x-coordinates for a PDF is not straightforward, and as such they are not included in the QSarray object initially. During the numerical convolution step, the gene set PDF is calculated at a number of points (equal to `QSarray$n.points`

) over a range defined by:

`c(path.mean - range, path.mean + range`

)

However, the resulting PDF is actually the *sum* of the individual gene PDFs, rather than the desired *average* PDF. Therefore the range which is stored in the resulting QSarray is divided by the number of genes in the pathway, `QSarray$path.size`

.

In addition, the width of the PDF can be expanded by the Variance Inflation Factor (VIF), which is equivalent to multiplying the range of the x-coordinates by the `sqrt(VIF)`

. If the parameter `addVIF=TRUE`

, the VIF calculatd using the `calcVIF`

method will be included in the calculation of the x-coordinates.

In general, the x-coordinates for a pathway are calculated for each point n using the following formula:

*x.n = ( seq(-1,1,length.out=N.points) * range * sqrt(VIF) ) + path.mean*

A numeric vector of length `QSarray$n.points`

.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ```
##create example data
eset = matrix(rnorm(500*20),500,20, dimnames=list(1:500,1:20))
labels = c(rep("A",10),rep("B",10))
##first 30 genes are differentially expressed
eset[1:30, labels=="B"] = eset[1:30, labels=="B"] + 1
geneSets = list(diff.set=1:30, base.set=31:60)
##Run qusage
set.results = qusage(eset, labels, "B-A", geneSets)
##Plot the PDF (see also: plotDensityCurves() )
x = getXcoords(set.results, 1)
y = set.results$path.PDF[,1]
plot(x,y, type="l")
``` |

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