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Last data update: 2014.03.03

R: A function that appends probe ids to a data frame containing...

mergeMCRProbes

R Documentation

A function that appends probe ids to a data frame containing MCRs

Description

This function takes a data frame generated by MCR and then append probe ids corresponding to each MCR as a column to the data frame.

Usage

mergeMCRProbes(mcr, rawData)

Arguments

`mcr`	`mcr` is a data frame generated by `MCR` that contains MCRs identified and other related data
`rawData`	`rawData` is a data frame with at least three columns. The first column should be probe ids, second the chromosome number the probes corresponding to, and the thrid the starting or ending chromosomal locations of the probes

Details

The mcr data frame passed must have the first column for chromosome numbers, the 7th column for the starting positions of the MCRs, and the 8th column for the ending positions of the MCRs.

Value

A data frame with MCRs and the corresponding probe ids and other data.

Note

The function is a contribution of The Center for Applied Cancer Science of Dana-Farber Cancer Institute

Author(s)

Jianhua Zhang

Examples

  data("segData")
  cghmcr <- cghMCR(segData, gapAllowed = 500, alteredLow = 0.20,
                   alteredHigh = 0.80, recurrence = 50)
  mcrs <- MCR(cghmcr)
  mcrs <- mergeMCRProbes(mcrs, segData[["data"]])

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(cghMCR)
Loading required package: DNAcopy
Loading required package: CNTools
Loading required package: tools
Loading required package: genefilter
Loading required package: limma
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/cghMCR/mergeMCRProbes.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mergeMCRProbes
> ### Title: A function that appends probe ids to a data frame containing
> ###   MCRs
> ### Aliases: mergeMCRProbes
> ### Keywords: manip
> 
> ### ** Examples
> 
>   data("segData")
>   cghmcr <- cghMCR(segData, gapAllowed = 500, alteredLow = 0.20,
+                    alteredHigh = 0.80, recurrence = 50)
>   mcrs <- MCR(cghmcr)
>   mcrs <- mergeMCRProbes(mcrs, segData[["data"]])
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>