inudge.plot.qq | R Documentation |
Produces a QQ-plot for visual inspection of quality of fit with regards to
the uniform Gaussian (iNUDGE) mixture model estimated using the function
inudge.fit
inudge.plot.qq(data, obj, resolution = 10, xlab = NULL, ylab = NULL, main = NULL, pch = NULL, ...)
data |
an R list of vector of normalized intensities (counts). Each element can correspond to particular chromosome. User can construct their own list containing only the chromosome(s) they want to analyze. |
obj |
a list object returned by |
resolution |
optional number of points used to sample the estimated density function. |
xlab |
optional x-axis label (see |
ylab |
optional y-axis label (see |
main |
optional plot title (see |
pch |
optional plotting symbol to use (see |
... |
additional graphical arguments to be passed to methods (see |
inudge.fit
, qqplot
library(DIME); # generate simulated datasets with underlying uniform and 2-normal distributions set.seed(1234); N1 <- 1500; N2 <- 500; rmu <- c(-2.25,1.5); rsigma <- c(1,1); rpi <- c(.10,.45,.45); a <- (-6); b <- 6; chr4 <- list(c(-runif(ceiling(rpi[1]*N1),min = a,max =b), rnorm(ceiling(rpi[2]*N1),rmu[1],rsigma[1]), rnorm(ceiling(rpi[3]*N1),rmu[2],rsigma[2]))); chr9 <- list(c(-runif(ceiling(rpi[1]*N2),min = a,max =b), rnorm(ceiling(rpi[2]*N2),rmu[1],rsigma[1]), rnorm(ceiling(rpi[3]*N2),rmu[2],rsigma[2]))); # analyzing chromosome 4 and 9 data <- list(chr4,chr9); # fit iNUDGE model with 2-normal components and maximum iteration =20 set.seed(1234); bestInudge <- inudge.fit(data, K=2, max.iter=20) # QQ-plot inudge.plot.qq(data,bestInudge);
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