deepSNV-class: deepSNV class.
In mg14/deepSNV-old: Detection of subclonal SNVs in deep sequencing data.

Description Author(s) See Also Examples

This class stores the contents of the deepSNV test. It is typically initialized with deepSNV. This class has the following slots:

p.val: The P-values of the test.
test: A matrix with the nucleotide counts in the test experiment. The column names of the nucleotide counts are A, T, C, G, - for the positivie strand and a, t, c, g, _ for the reverse.
control: A matrix with the nucleotide counts in the control experiment. The column names must be the same as for the test.
coordinates: A data.frame with the genomic coordinates chr and pos, and other columns, if desired.
dirichlet.prior: A matrix with the nucleotide-specific Dirichlet prior
pseudo.count: The pseudo count if used)
alternative: A string with the alternative used in the test.
nucleotides: A character vector with the nucleotides tested.
regions: A data.frame with columns chr, start, and stop.
files: A list with two entries test and control storing the filenames (if the object was initialized from two bam-files).
combine.method: The method for combining p-values as a character string.
model: The statistical model, either bin for binomial, or betabin for beta-binomial
over.dispersion: If the model is beta-binomial, the first parameter for the beta-binomial model, which is shared across sites.
call: The last function call to deepSNV.
log.lik: The log likelihood of the data under the null hypothesis. (Excluding zeros on the opposite site under a one-sided test.)

Moritz Gerstung

deepSNV

## Short example with 2 SNVs at frequency ~10%
regions <- data.frame(chr="B.FR.83.HXB2_LAI_IIIB_BRU_K034", start = 3120, stop=3140)
ex <- deepSNV(test = system.file("extdata", "test.bam", package="deepSNV"), control = system.file("extdata", "control.bam", package="deepSNV"), regions=regions, q=10)
show(ex)   # show method
plot(ex)   # scatter plot
summary(ex)   # summary with significant SNVs
ex[1:3,]   # subsetting the first three genomic positions
tail(test(ex, total=TRUE))   # retrieve the test counts on both strands
tail(control(ex, total=TRUE))

## Not run: Full example with ~ 100 SNVs. Requires an internet connection, but try yourself.
# regions <- data.frame(chr="B.FR.83.HXB2_LAI_IIIB_BRU_K034", start = 2074, stop=3585)
# HIVmix <- deepSNV(test = "http://www.bsse.ethz.ch/cbg/software/deepSNV/data/test.bam", control = "http://www.bsse.ethz.ch/cbg/software/deepSNV/data/control.bam", regions=regions, q=10)
data(HIVmix) # attach data instead..
show(HIVmix)
plot(HIVmix)
head(summary(HIVmix))