rranges: Simulate a GRanges or RangedData object
In humarray: Simplify Analysis and Annotation of Human Microarray Datasets

Description Usage Arguments Value Examples

For testing purposes, this function will generate a S4 ranged object based on the human genome. The default is to produce ranges selected from chromosomes, with probability of a position in each chromosome equal to the length of that chromosome versus the whole genome. The maximum position allocated within each chromosome will be within the length bounds of that chromosome. You can specify SNPs (ie., start =end), but the default is for random ranges. You can alter the UCSC build to base the chromosome lengths on, and you can specify whether chromosomes should appear as chr1,chr2,... versus 1,2,..

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rranges(n = 10, SNP = FALSE, chr.range = 1:26, chr.pref = FALSE,
  order = TRUE, equal.prob = FALSE, GRanges = TRUE, build = NULL,
  fakeids = FALSE)

`n`	integer, number of rows to simulate
`SNP`	logical, whether to simulate SNPs (width 1, when SNPs=TRUE) or just ranges (when SNP=FALSE)
`chr.range`	integer vector of values from 1 to 26, to specify which chromosomes to include in the simulated object. 23-26 are X,Y,XY,MT respectively.
`chr.pref`	logical, if TRUE chromosomes will be coded as chr1,chr2,..., versus 1,2,.. when chr.pref=FALSE
`order`	logical, if TRUE the object returned will be in genomic order, otherwise the order will be randomized
`equal.prob`	logical, when FALSE (default), random positions will be selected on chromosomes chosen randomly according to the their length (i.e, assuming every point on the genome has equal probability of being chosen. If equal.prob=TRUE, then chromosomes will be selected with equal probability, so you could expect just as many MT (mitochondrial) entries as Chr1 entries.
`GRanges`	logical, if TRUE the returned object will be GRanges format, or if FALSE, then RangedData format
`build`	character, to specify the UCSC version to use, which has a small effect on the chromosome lengths. Use either "hg18" or "hg19". Will also accept build number, e.g, 36 or 37.
`fakeids`	logical, whether to add rownames with random IDs (TRUE) or leave rownames blank (FALSE). If SNP=TRUE, then ids will be fake rs-ids.

returns a ranged object (GRanges or RangedData) containing data for 'n' simulated genomic ranges, such as SNPs or CNVs across chromosomes in 'chr.range', using UCSC 'build'.

rranges()
rr <- rranges(SNP=TRUE,chr.pref=TRUE,fakeids=TRUE)
width(rr) # note all have width 1
rr
tt <- table(chrm(rranges(1000)))
print(tt/sum(tt)) # shows frequencies at which the chr's were sampled
tt <- table(chrm(rranges(1000,equal.prob=TRUE)))
print(tt/sum(tt)) # shows frequencies at which the chr's were sampled