snp.refine.boundary: Refine Segment Boundaries

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

Description

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 <[e-mail]>

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)

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