nudge.plot.comp {DIME}

Plot NUDGE Individual Components

Description

Plot each estimated individual components of NUDGE model (mixture of uniform and 1-normal) fitted using nudge.fit.

Usage

nudge.plot.comp(data, obj, new.plot = TRUE, legpos = NULL, xlim = NULL,
  ylim = NULL, xlab = NULL, ylab = NULL, main = NULL, lwd = NULL, ...)

Arguments

data

an R list of vector of normalized intensities (counts). Each element can correspond to a particular chromosome. User can construct their own list containing only the chromosome(s) they want to analyze.

obj

a list object returned by nudge.fit function.

new.plot

an R list of vector of normalized intensities (counts). Each object can correspond to particular chromosome that one want to fit.

legpos

optional vector of (x,y) location for the legend position

xlim

optional x-axis limit (see par).

ylim

optional y-axis limit (see par).

xlab

optional x-axis label (see par).

ylab

optional y-axis label (see par).

main

optional plot title (see par).

lwd

optional line width for lines in the plot (see par).

...

additional graphical arguments to be passed to methods (see par).

Details

The components representing differential data are denoted by asterisk (*) symbol on the plot legend.

See Also

nudge.plot.mix, inudge.plot.comp, nudge.plot.fit, nudge.plot.qq, DIME.plot.fit, gng.plot.fit.

Examples

library(DIME);
# generate simulated datasets with underlying uniform and 1-normal components
set.seed(1234);
N1 <- 1500; N2 <- 500; rmu <- c(1.5); rsigma <- c(1); 
rpi <- c(.10,.90); a <- (-6); b <- 6; 
chr1 <- c(-runif(ceiling(rpi[1]*N1),min = a,max =b),
  rnorm(ceiling(rpi[2]*N1),rmu[1],rsigma[1]));
chr4 <- c(-runif(ceiling(rpi[1]*N2),min = a,max =b),
  rnorm(ceiling(rpi[2]*N2),rmu[1],rsigma[1]));  
# analyzing chromosome 1 and 4
data <- list(chr1,chr4);

# fit NUDGE model with maximum iterations = 20
set.seed(1234);
bestNudge <- nudge.fit(data, max.iter=20);

# plot individual components of NUDGE
nudge.plot.comp(data,bestNudge);