deepSNV-class: deepSNV class.
In gerstung-lab/deepSNV: Detection of subclonal SNVs in deep sequencing data.

deepSNV-class

R Documentation

deepSNV class.

Description

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.)

Author(s)

Moritz Gerstung

Examples

## 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))

gerstung-lab/deepSNV documentation built on June 3, 2022, 3:05 p.m.