示例#1
0
文件: cr.go 项目: mingzhi/pileup
// Calculate covariance of rates.
func (cmd *cmdCr) calcCr(pis []Pi, profile []profiling.Pos, posType byte, maxl int) (covs []Covariance) {
	corrs := make([]Covariance, maxl)
	for i := 0; i < maxl; i++ {
		corrs[i] = correlation.NewBivariateCovariance(false)
	}

	for i := 0; i < len(pis); i++ {
		p1 := pis[i]
		pos1 := profile[p1.Pos]
		if checkPosType(posType, pos1.Type) {
			for j := i; j < len(pis); j++ {
				p2 := pis[j]
				pos2 := profile[p2.Pos]

				distance := p2.Pos - p1.Pos
				if distance < 0 {
					distance = -distance
				}
				if distance >= maxl {
					break
				}

				if checkPosType(posType, pos2.Type) {
					x, y := p1.Pi(), p2.Pi()
					corrs[distance].Increment(x, y)
				}
			}
		}

	}

	covs = corrs
	return
}
示例#2
0
// NewCovariances create a new Covariances
func NewCovariances(maxl int) *Covariances {
	cc := Covariances{}
	for i := 0; i < maxl; i++ {
		bc := correlation.NewBivariateCovariance(false)
		cc.corrs = append(cc.corrs, bc)
	}
	return &cc
}
示例#3
0
// Increment add x and y arrays, which separate at distance l.
func (c *Calculator) Increment(xArr, yArr []float64, l int) {
	if l < c.MaxL {
		// calculate covariance of x and y.
		cov := correlation.NewBivariateCovariance(false)
		for i := range xArr {
			x, y := xArr[i], yArr[i]
			cov.Increment(x, y)
		}

		c.Cs.Increment(l, cov.GetResult())
		c.Ct.AppendAt(l, cov)
		c.Cr.Increment(l, cov.MeanX(), cov.MeanY())

	}
}