View source: R/nudge.classify.R
nudge.classify | R Documentation |
Classifies observed data into differential and non-differential groups based on NUDGE model.
nudge.classify(data, obj, obj.cutoff = 0.1, obj.sigma.diff.cutoff = NULL, obj.mu.diff.cutoff = 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 |
obj.cutoff |
optional local fdr cutoff for classifying data into differential and non-differential groups based on NUDGE model. |
obj.sigma.diff.cutoff |
optional cut-off for standard deviation of the normal component in NUDGE model to be designated as representing differential. |
obj.mu.diff.cutoff |
optional cut-off for standard deviation of the normal component in NUDGE model to be designated as representing differential. |
A list object passed as input with additional element $class containing vector of classifications for all the observations in data. A classification of 1 denotes that the data is classified as differential with fdr < obj.cutoff.
mu.diff.cutoff |
normal component with mean > mu.diff.cutoff was used to represent differential component. |
sigma.diff.cutoff |
normal component with standard deviation > sigma.diff.cutoff was used to represent differential component. |
Cenny Taslim taslim.2@osu.edu, with contributions from Abbas Khalili khalili@stat.ubc.ca, Dustin Potter potterdp@gmail.com, and Shili Lin shili@stat.osu.edu
nudge.fit
library(DIME); # generate simulated datasets with underlying uniform and 1-normal components set.seed(1234); N1 <- 1500; N2 <- 500; rmu <- c(1.5); rsigma <- c(1); rpi <- c(.10,.90); a <- (-6); b <- 6; chr1 <- c(-runif(ceiling(rpi[1]*N1),min = a,max =b), rnorm(ceiling(rpi[2]*N1),rmu[1],rsigma[1])); chr4 <- c(-runif(ceiling(rpi[1]*N2),min = a,max =b), rnorm(ceiling(rpi[2]*N2),rmu[1],rsigma[1])); # analyzing chromosome 1 and 4 data <- list(chr1,chr4); # fit NUDGE model with maximum iterations = 20 only set.seed(1234); test <- nudge.fit(data, max.iter=20) # vector of classification. 1 represents differential, 0 denotes non-differential nudgeClass <- test$class;
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