aCGH.process {aCGH} | R Documentation |
This function takes object of class aCGH
, and filters clones based on their mapping information and proportion missing. It also average duplicated clones and reports quality statistic.
aCGH.process(aCGH.obj, chrom.remove.threshold = 24, prop.missing = 0.25, sample.quality.threshold = 0.4, unmapScreen=TRUE, dupRemove = TRUE)
aCGH.obj |
Object of class aCGH |
chrom.remove.threshold |
Chromosomes are ordered and numbered as usual, except for X and Y chromosome, which in for Homo sapiens genome have numbers 23 and 24 repsectivelly, in for Mus musculus 20 and 21, etc. |
prop.missing |
Clones are screened out and if the proportion
missing in the samples is prop.missing they are removed. |
sample.quality.threshold |
Mark those samples that have their
proportion of missing values sample.quality.threshold . |
unmapScreen |
Indicator for whether clones with incomplete mapping information should be removed from the dataset. Note that leaving them in may cause plotting routines fail. Defaults to TRUE |
dupRemove |
Indicator for whether clones with duplicate names should be averaged and removed from the dataset leaving only one occurence of each duplicated set.Defaults to TRUE |
Object of class aCGH
.
Jane Fridlyand, Peter Dimitrov
aCGH
datadir <- system.file(package = "aCGH") datadir <- paste(datadir, "/examples", sep="") clones.info <- read.table(file = file.path(datadir, "clones.info.ex.txt"), header = TRUE, sep = "\t", quote="", comment.char="") log2.ratios <- read.table(file = file.path(datadir, "log2.ratios.ex.txt"), header = TRUE, sep = "\t", quote="", comment.char="") pheno.type <- read.table(file = file.path(datadir, "pheno.type.ex.txt"),header = TRUE, sep = "\t", quote="", comment.char="") ex.acgh <- create.aCGH(log2.ratios, clones.info, pheno.type) ex.acgh <- aCGH.process(ex.acgh, chrom.remove.threshold = 23, prop.missing = .25, sample.quality.threshold = .4, unmapScreen=TRUE, dupRemove = FALSE) ex.acgh