Refine the segment boundaries based on the grid of heterozygous probes
by all probes with LRR data. We do not recommend to perform this step
except in the case that the segment boundaries need to be aligned well
on the same grid of probes for downstream analysis.
Usage
snp.refine.boundary(data, segs.stat)
Arguments
data
a data frame containing log2ratio and log2mBAF data generated
by snp.cnv.data.
segs.stat
a data frame containing segment locations and summary statistics
resulting from cnv.call.
Value
A data frame with the same columns as the one generated by
cnv.call with the columns posStart,
posEnd, length, chrIdxStart,
chrIdxEnd and numProbe updated accordingly.
Author(s)
Zhongyang Zhang <zhongyang.zhang@mssm.edu>
See Also
snp.cnv.data, cnv.call
Examples
## Not run:
## download snp.data.RData
url <- "https://zhangz05.u.hpc.mssm.edu/saasCNV/data/snp.data.RData"
tryCatch({download.file(url=url, destfile="snp.data.RData")
}, error = function(e) {
download.file(url=url, destfile="snp.data.RData", method="curl")
})
## If download.file fails to download the data, please manually download it from the url.
load("snp.data.RData")
data(snp.cnv)
snp.cnv.refine <- snp.refine.boundary(data=snp.data, segs.stat=snp.cnv)
## End(Not run)
## how the results look like
data(snp.cnv.refine)
head(snp.cnv.refine)