calc_q1: calc_q1...
In mdavy86/polymapR: Linkage Analysis in Outcrossing Polyploids
View source: R/aiding_functions.R
Description
Calculate q1 quality score. q1 is a measure of the fit of selfit.
It is based on Pvalue and the fraction of valid F1 scores. If either is below their
threshold the q1 value is 0. Also, if bestParentfit is different from bestfit this indicates a segregation distortion.
Usage
1
2
calc_q1(Pvalue, fracInvalid, bestfit, bestParentfit, Pvalue_threshold,
fracInvalid_threshold)
Arguments
Pvalue
P-value of bestParentfit segtype
fracInvalid
Fraction invalid scores of bestParentfit segtype
bestfit
segtype of best fit of population
bestParentfit
segtype of best fit of parents
Pvalue_threshold
Threshold P-value of bestParentfit segtype
fracInvalid_threshold
a maximum threshold for the fracInvalid of the bestParentfit segtype
(with a larger fraction of invalid dosages in the F1 the q1 quality parameter will be set to 0)
mdavy86/polymapR documentation built on May 25, 2019, 9:35 p.m.
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View source: R/aiding_functions.R
Description
Calculate q1 quality score. q1 is a measure of the fit of selfit. It is based on Pvalue and the fraction of valid F1 scores. If either is below their threshold the q1 value is 0. Also, if bestParentfit is different from bestfit this indicates a segregation distortion.
Usage
1 2 | calc_q1(Pvalue, fracInvalid, bestfit, bestParentfit, Pvalue_threshold,
fracInvalid_threshold)
|
Arguments
Pvalue |
P-value of bestParentfit segtype |
fracInvalid |
Fraction invalid scores of bestParentfit segtype |
bestfit |
segtype of best fit of population |
bestParentfit |
segtype of best fit of parents |
Pvalue_threshold |
Threshold P-value of bestParentfit segtype |
fracInvalid_threshold |
a maximum threshold for the fracInvalid of the bestParentfit segtype (with a larger fraction of invalid dosages in the F1 the q1 quality parameter will be set to 0) |
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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