saasCNV (version 0.3.4)

GC.adjust: GC Content Adjustment

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.

Value

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.

Details

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

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)