chrSegment {fcros} | R Documentation |
This function allows to segment a chromosome data
chrSegment(chrData, nd = 10)
chrData |
A chromosome data obtained from an output of the function
dataSummary(): |
nd |
The acceptable number of non-detected probes which can separate two
significant probes in a segment. Default setting value is 10: |
This function returns a data frame containing 6 information for each segment
idStart |
The start position indexes associated with segments |
idEnd |
The End position indexes associated with segments |
lBounds |
The lower bound positions associated with segments |
uBounds |
The upper bound positions associated with segments |
segL2R |
The change values associated with segments |
segProba |
The probabilities associated with segments |
Doulaye Dembele doulaye@igbmc.fr
Dembele D, Analysis of high biological data using their rank values, Stat Methods Med Res, accepted for publication, 2018
# load CGH data and info files data(cghData) rownames(cghData) <- cghData[,1] data(cghInfo) noms <- colnames(cghData) m <- length(noms) samp <- noms[2:m] # associate statistics with probes in the dataset af <- pfcoMod(cghData, samp, log2.opt = 0, trim.opt = 0.25) chromosomes = c(7:9) alpha <- 0.05 # summarize results for each chromosome xinfo2 <- dataSummary(af, cghInfo, chromosomes, alpha) # focused on chromosome 7 data idx <- which(xinfo2$xinfo.s$Chromosome == "7") chrData <- xinfo2$xinfo.s[idx, ] # segment chromosome 7 data chrSeg <- chrSegment(chrData, nd = 15) # show first 10 segment results chrSeg[1:10,]