cr2pts {onemap} | R Documentation |
An interface between R and the C routine that performs the two-point analysis. Given the type of segregation of the two markers, this function creates the corresponding vectors and matrices that are necessary to the C routine and makes a call to it.
cr2pts(mrk1, mrk2, segr.type1, segr.type2)
mrk1 |
a vector containing the genotypes of all individuals for the first marker. |
mrk2 |
a vector containing the genotypes for the second marker. |
segr.type1 |
the type of segregation of the first marker
(mrk1 ). |
segr.type2 |
the type of segregation of the second marker
(mrk2 ). |
Returns a list with the following components:
r |
a vector with the maximum likelihood estimates of the
recombination fraction between both markers, under the 4
possible assignments. |
like |
a vector with the likelihood of the data under each of the
4 assignments. |
posterior |
a vector with the posterior probability of each of
the 4 assignments. |
LOD |
a vector with the LOD Score for the 4 assignments -
the base 10 logarithm of the ratio of the maximum likelihood and the
likelihood under the null hypothesis of no linkage. |
Gabriel R A Margarido, gramarga@esalq.usp.br
Wu, R., Ma, C.-X., Painter, I. and Zeng, Z.-B. (2002) Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species. Theoretical Population Biology 61: 349-363.
est.rf.2pts
; for details concerning the types of
segregation, see mrktype
.
data(example_out) # getting values marker1 <- example_out$geno[,1] marker2 <- example_out$geno[,2] segr.type1 <- example_out$segr.type[1] segr.type2 <- example_out$segr.type[2] # two-point analysis cr2pts(marker1,marker2,segr.type1,segr.type2)