annotexample: Annotation table for ROMA CGH platform and human genome...

In KrasnitzLab/CNprep: Pre-process DNA Copy Number (CN) Data for Detection of CN Events

Annotation table for ROMA CGH platform and human genome version 17.

Description

Whole genome annotation table using Representational Oligonucleotide Microarray Analysis (ROMA) CGH platform, human genome version 17.

Usage

data(annotexample)

Format

a data.frame with 83055 observations on the following 3 variables.

PROBEID

a character vector of probe names.

CHROM

a numeric vector, used as integer, of chromosome positions.

CHROM.POS

a numeric vector, used as integer, of genomic positions.

Details

The values in the chromosome column are all integer, with 23 corresponding to X, 24 to Y and 25 to a set of non-human test probes.

Value

a data.frame with 83055 observations on the following 3 variables.

PROBEID

a character vector of probe names.

CHROM

a numeric vector, used as integer, of chromosome positions.

CHROM.POS

a numeric vector, used as integer, of genomic positions.

Source

GEO accession GPL9775, http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL9775

See Also

• CNpreprocessing for pre-process DNA copy number (CN) data for detection of CN events.

• makeCNPmask for creating a mask given a set of copy number events.

• applyCNPmask for applying a mask to a set of copy number events.

Examples

## Loading annotation table dataset
data(annotexample)

## Loading other datasets
data(ratexample)
data(segexample)
data(normsegs)

## How to use annotexample, when segment table does not have columns 
## of integer postions in terms of measuring units(probes), such 
## as "mysegs" below 

mysegs <- segexample[,c(1,5:12)]

## Analysis limited to chromosomes 1 and 2
## The bsTimes variable should be higher for a real analysis
segtable <- CNpreprocessing(segall=mysegs, ratall=ratexample, idCol="ID",
    chromCol="chrom", bpStartCol="chrom.pos.start", bpEndCol="chrom.pos.end",
    annot=annotexample, annotStartCol="CHROM.POS", annotEndCol="CHROM.POS",
    annotChromCol = "CHROM", blsize = 50, minJoin = 0.25, cWeight = 0.4, 
    bsTimes = 3, chromRange = 1:2,  nJobs = 1, modelNames = "E", 
    normalLength = normsegs[,1], normalMedian = normsegs[,2])

KrasnitzLab/CNprep documentation built on May 28, 2022, 8:32 p.m.