Description Usage Arguments Value Author(s) References See Also Examples
Transform read depth information into log2ratio and log2mBAF that we use for joint segmentation and CNV calling.
1 |
vcf |
a data frame constructed from a vcf file. See |
min.chr.probe |
the minimum number of probes tagging a chromosome for it to be passed to the subsequent analysis. |
verbose |
logical. If more details to be output. Default is |
A data frame containing the log2raio and log2mBAF values for each probe site.
Zhongyang Zhang <zhongyang.zhang@mssm.edu>
Staaf, J., Vallon-Christersson, J., Lindgren, D., Juliusson, G., Rosenquist, R., Hoglund, M., Borg, A., Ringner, M. (2008) Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios. BMC bioinformatics, 9:409.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ## load a data frame constructed from a vcf file with vcf2txt
## Not run:
## download vcf_table.txt.gz
url <- "https://zhangz05.u.hpc.mssm.edu/saasCNV/data/vcf_table.txt.gz"
tryCatch({download.file(url=url, destfile="vcf_table.txt.gz")
}, error = function(e) {
download.file(url=url, destfile="vcf_table.txt.gz", method="curl")
})
## If download.file fails to download the data, please manually download it from the url.
vcf_table <- read.delim(file="vcf_table.txt.gz", as.is=TRUE)
seq.data <- cnv.data(vcf=vcf_table, min.chr.probe=100, verbose=TRUE)
## End(Not run)
## see how seq.data looks like
data(seq.data)
head(seq.data)
|
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