processCGH {snapCGH}R Documentation

Process data in an MAList

Description

This function takes object of class MAList and it re-orderes and filters clones based on their mapping information and proportion missing. It also average duplicated clones and imputes missing values for clones that are still NA after the filetering step. Note that imputation will only take place if duplicated clones are removed.

Usage

processCGH(input, maxChromThreshold = 22, minChromThreshold
                 = 1, method.of.averaging = NULL, ID = "ID", prop.missing = 0.1)

Arguments

input Object of class MAList or RGList
maxChromThreshold 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. Remove chromosomes from segmentation analysis which are greater than this value.
minChromThreshold 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. Remove chromosomes from segmentation analysis which re lower than this value.
method.of.averaging If left as the default no combining of replicate spots takes place. Other wise this should specify a function which takes a vector of duplicates and combines them into a single value.
ID Name of column in RG\$genes corresponding to the clone names. For most data the default will work, however for affy data the value for ID should be "CloneName"
prop.missing For each probe the proportion of NA's is calculated, and the probe is kept for further analysis if the proportion of NA's is less than missing.prop

Value

Object of class SegList

Author(s)

Jane Fridlyand, Peter Dimitrov, John Marioni and Mike Smith

See Also

MAList


[Package snapCGH version 1.4.0 Index]