segments.summary {DNAcopy} | R Documentation |
This program computes the standard deviation, median and the mad of the data for each segment found by the CBS algorithm.
segments.summary(x)
x |
an object of class DNAcopy |
a data frame with nine columns. The sd, median and mad of each segment is added to the six columns from the segment command.
Venkatraman E. Seshan ves2111@columbia.edu
# test code on an easy data set set.seed(25) genomdat1 <- rnorm(500, sd=0.1) + rep(c(-0.2,0.1,1,-0.5,0.2,-0.5,0.1,-0.2),c(137,87,17,49,29,52,87,42)) genomdat2 <- rnorm(500, sd=0.1) + rep(c(-0.2,0.1,1,-0.5,0.2,-0.5,0.1,-0.2),c(137,87,17,49,29,52,87,42)) genomdat1[sample(1:500,5)] <- NA chrom <- rep(1:2,c(290,210)) maploc <- c(1:290,1:210) test1 <- segment(CNA(cbind(genomdat1,genomdat2), chrom, maploc)) segments.summary(test1)