subsetCNR | R Documentation |
This function pulls out a section of the genome for further analysis.
subsetCNR( cnr, bins = NULL, genes = NULL, chrom = NULL, start = NULL, end = NULL, ... )
cnr |
a cnr bundle |
bins |
a vector of bins to keep |
genes |
a vector of genes to keep |
chrom |
a vector of chromosomes, or single chromosome if genomic coordinates are used |
start |
a start position |
end |
an end position |
... |
additional parameters e.g. padding to add bins when coordinates are used |
Returns a cnr object with only the desired bins. This function also subsets the gene index and chromInfo as well
data(cnr) data(segCol) ## subset based on bins bins1.100 <- subsetCNR(cnr, bins = 1:100) ## subset based on genes genes.3 <- subsetCNR(cnr, genes = c("CDK4", "MDM2", "HMGA2", "TP53")) ## subset based on chromosomes chrom6.12 <- subsetCNR(cnr, chrom = c(6, 12)) ## subset based on genomic coordinates chrom12q13.15 <- subsetCNR(cnr, chrom = 12, start = 46000000, end = 71000000)
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