normsegs | R Documentation |
A table of segment lengths and log copy number ratios for a large set of human diploid genomes.
data(normsegs)
a matrix
with 43497 rows/segments and 2 columns/variables.
The 2 columns are:
length
a numeric
vector
, used as integer, of
segment genomic length
segmedian
a numeric
vector
of segment
median computed from log copy number ratio
The table originates in a set of copy number profiles of over 1000 individuals, obtained using Representational Oligonucleotide Microarray Analysis (ROMA) technology. To ensure ploidy of 2 segments from X and Y chromosomes and segments shorter than 5Mb were excluded.
a matrix
with 43497 rows/segments and 2 columns/variables.
The 2 columns are:
length
a numeric
vector
, used as integer, of
segment genomic length
segmedian
a numeric
vector
of segment
median computed from log copy number ratio
Sebat J, et al. Strong association of de novo copy number mutations with autism. Science. 2007 Apr 20;316(5823):445-9. Epub 2007 Mar 15.
CNpreprocessing
for pre-process DNA copy number (CN)
data for detection of CN events.
## Loading log ratio dataset data(segexample) ## Load datasets data(segexample) data(ratexample) data(normsegs) ## Preprocess segments for WZ3 sample segtable <- CNpreprocessing(segall=segexample[segexample[,"ID"] == "WZ3",], ratall = ratexample, idCol = "ID", startCol = "start", endCol="end", chromCol = "chrom", bpStartCol = "chrom.pos.start", bpEndCol = "chrom.pos.end", blsize = 50, minJoin = 0.30, cWeight = 0.4, bsTimes = 40, chromRange = 1:22, modelNames = "E", normalLength = normsegs[,1], normalMedian = normsegs[,2])
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