GC.adjust {saasCNV} | R Documentation |
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 |
gc |
A data frame containing three columns: |
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 <zhongyang.zhang@mssm.edu>
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
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)