check.trait {GenABEL} | R Documentation |
This function check for outliers (using FDR framework) and plots the raw data.
check.trait(trait, data, fdrate = 0.05, graph = TRUE, binshow = FALSE, qoption = "bh95")
trait |
name (or list of names) of trait(s) to be checked |
data |
gwaa.data object or data frame containing the trait |
fdrate |
false discovery rate to apply for QC |
graph |
if graphical output should be produced |
binshow |
if binary traits should be plotted |
qoption |
how to compute q-values (not implemented, currently using only BH95) |
The P-value that a particulat measurment is an outlier is compted as folowing. Consider trait vector Y with particulat i^{th} measurment denodet as y_i. Let Y(-i) is vector, which is the same as Y, except that i^{th} measurment is dropped. Then Chi-square for measurment i is computed as
Chi_{i} = (mean(Y(-i)) - y_i)^2/var(Y(-i))
P-value is computed using 1 d.f., and the vector of P-values enters FDR computation procedure (BH95 by default).
No value returned, output is made to the screen and graphical device.
Yurii Aulchenko
data(srdta) check.trait("qt3",data=srdta) n <- names(srdta@phdata) check.trait(n,data=srdta)