aCGH.process {aCGH} | R Documentation

## Process data in aCGH object

### Description

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.

### Usage

    aCGH.process(aCGH.obj, chrom.remove.threshold = 24,
                     prop.missing = 0.25, sample.quality.threshold = 0.4,
                     unmapScreen=TRUE, dupRemove = TRUE)

### Arguments

`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

### Value

Object of class `aCGH`.

### Author(s)

Jane Fridlyand, Peter Dimitrov

### See Also

`aCGH`

### Examples

    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

[Package aCGH version 1.16.0 Index]