mppR (version 1.5.0)

QTL_select: QTL candidates selection

Description

Selection of QTL candidate positions.

Usage

QTL_select(Qprof, threshold = 3, window = 50, verbose = TRUE)

Value

Return:

QTL

Data.frame of class QTLlist with five columns : 1) QTL marker names; 2) chromosomes; 3) interger position indicators on the chromosome; 4) positions in centi-Morgan; and 5) -log10(p-values).

Arguments

Qprof

Object of class QTLprof returned by the function mpp_SIM or mpp_CIM.

threshold

Numeric value representing -log10(p-value) threshold above which a position can be considered as a QTL candidate. Default = 3.

window

Numeric value in centi-Morgan representing the minimum distance between two selected positions. Default = 50.

verbose

Logical value specifying if the detection of no QTL should be printed. Default = TRUE.

Details

The function select QTL positions that are above the given threshold per chromosome. Once a position has been selected, and exclusion window is set around that position. Positions falling into that region will not be candidate anymore. The search continue until there is no more candidate position above the threshold.

References

This function is a modification of the QTL.reduce function coming from the Biometris pipepline.

RAP (R Analytical Pipeline) (V0.9.1) May 2011

Authors: Paul Eilers (1), Gerrit Gort (1), Sabine Schnabel (1), Lucia Gutierrez(1, 2), Marcos Malosetti(1), Joost van Heerwaarden, and Fred van Eeuwijk(1)

(1) Wageningen University and Research Center, Netherlands (2) Facultad de Agronomia, UDELAR, Uruguay

See Also

mpp_SIM, mpp_CIM, mpp_perm

Examples

data(mppData)

SIM <- mpp_SIM(mppData)

QTL <- QTL_select(Qprof = SIM, threshold = 3)