Man pages for aCGH
Classes and functions for Array Comparative Genomic Hybridization data
| aCGH | Class aCGH |
| aCGH.process | Process data in aCGH object |
| aCGH.read.Sprocs | Create object of class "aCGH" from Sproc files |
| aCGH.test | Testing association of aCGH clones with censored or... |
| clusterGenome | clustering and heatmap |
| colorectal | Colorectal array CGH dataset |
| computeSD.func | Function to estimate experimental variability of a sample |
| fga.func | Function to compute fraction of genome altered for each... |
| findAber.func | Function to determines focal aberrations |
| findAmplif.func | Function to determine high level amplifications |
| find.genomic.events | Finds the genomic events associated with each of the array... |
| find.hmm.states | Determines states of the clones |
| findOutliers.func | Function to identify outlier clones |
| findTrans.func | Funtion identifying the transitions |
| gainLoss | Function to compute proportion of gains and losses for each... |
| heatmap | Creates heatmap array CGH objects |
| human.chrom.info.Jul03 | Basic Chromosomal Information for UCSC Human Genome Assembly... |
| human.chrom.info.May04 | Basic Chromosomal Information for UCSC Human Genome Assembly... |
| impute.HMM | Imputing log2 ratios using HMM |
| impute.lowess | Imputing log2 ratios |
| mergeFunc | Funtion to merge states based on their state means |
| mergeLevels | mergeLevels |
| plotFreqStat | frequency plots and significance analysis |
| plotGenome | Plots the genome |
| plotHmmStates | Plotting the estimated hmm states and log2 ratios for each... |
| plotSummaryProfile | plotSummaryProfile |
| states.hmm.func | A function to fit unsupervised Hidden Markov model |
| summarize.clones | Extracting summary information for all clones |
| threshold.func | Function to indicate gain or loss for each clone for each... |
