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aCGH (version 1.50.0)

Classes and functions for Array Comparative Genomic Hybridization data.

Description

Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.

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Version

Version

1.50.0

License

GPL-2

Maintainer

Last Published

February 15th, 2017

Functions in aCGH (1.50.0)

Testing association of aCGH clones with censored or continuous outcomes

clustering and heatmap

Imputing log2 ratios

Funtion to merge states based on their state means

findAmplif.func

Function to determine high level amplifications

findOutliers.func

Function to identify outlier clones

plotSummaryProfile

plotSummaryProfile

states.hmm.func

A function to fit unsupervised Hidden Markov model

Function to compute fraction of genome altered for each sample

find.genomic.events

Finds the genomic events associated with each of the array CGH samples

human.chrom.info.May04

Basic Chromosomal Information for UCSC Human Genome Assembly May 2004 freeze

Imputing log2 ratios using HMM

Process data in aCGH object

aCGH.read.Sprocs

Create object of class "aCGH" from Sproc files

frequency plots and significance analysis

Colorectal array CGH dataset

Function to estimate experimental variability of a sample

Funtion identifying the transitions

Function to compute proportion of gains and losses for each clones

Plotting the estimated hmm states and log2 ratios for each sample.

Plots the genome

find.hmm.states

Determines states of the clones

Function to determines focal aberrations

Creates heatmap array CGH objects

human.chrom.info.Jul03

Basic Chromosomal Information for UCSC Human Genome Assembly July 2003 freeze

summarize.clones

Extracting summary information for all clones

Function to indicate gain or loss for each clone for each sample