GC.adjust: GC Content Adjustment

In saasCNV: Somatic Copy Number Alteration Analysis Using Sequencing and SNP Array Data

Description

This function adjusts log2ratio by GC content using LOESS.

Usage

GC.adjust(data, gc, maxNumDataPoints = 10000)

Arguments

data	A data frame generated by cnv.data or snp.cnv.data.
gc	A data frame containing three columns: chr, position and GC. See the example data below for details.
maxNumDataPoints	The maximum number of data points used for loess fit. Default is 10000.

Details

The method for GC content adjustment was adopted from CNAnorm (Gusnato et al. 2012).

Value

A data frame containing the log2ratio (GC adjusted) and log2mBAF values for each probe site in the same format as generated by cnv.data or snp.cnv.data. The original log2ratio is renamed as log2ratio.woGCAdj. The GC-adjusted log2ratio is nameed as log2ratio.

Note

This function is optional in the analysis pipeline and is now in beta version.

Author(s)

Zhongyang Zhang <[e-mail]>

References

Gusnanto, A, Wood HM, Pawitan Y, Rabbitts P, Berri S (2012) Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data. Bioinformatics, 28:40-47.

See Also

cnv.data, snp.cnv.data

Examples

## CNV data generated by cnv.data
data(seq.data)
head(seq.data)

## Not run: 
## an example GC content file
url <- "https://zhangz05.u.hpc.mssm.edu/saasCNV/data/GC_1kb_hg19.txt.gz"
tryCatch({download.file(url=url, destfile="GC_1kb_hg19.txt.gz")
         }, error = function(e) {
          download.file(url=url, destfile="GC_1kb_hg19.txt.gz", method="curl")
         })
## If download.file fails to download the data, please manually download it from the url.

gc <- read.delim(file = "GC_1kb_hg19.txt.gz", as.is=TRUE)
head(gc)

## GC content adjustment
seq.data <- GC.adjust(data = seq.data, gc = gc, maxNumDataPoints = 10000)
head(seq.data)

## End(Not run)

saasCNV documentation built on May 1, 2019, 7:49 p.m.