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)
## 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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