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deepSNV (version 1.18.3)

summary: Summary of a deepSNV object

Description

Tabularize significant SNVs by evalutating the p-values of the deepSNV test.

Summary for deepSNV object

Usage

"summary"(object, sig.level = 0.05, adjust.method = "bonferroni", fold.change = 1, value = c("data.frame", "VCF"))

Arguments

object
A deepSNV-class object.
sig.level
The desired significance level.
adjust.method
The adjustment method for multiple testing corrections. See p.adjust for details. Set to NULL, for no adjustment. Default "bonferroni".
fold.change
The minimal fold change required of the relative frequency. Default 1.
value
String. The type of the returned object. Either "data.frame" for a data.frame (default) or "VCF" for an ExtendedVCF-class object.

Value

If value="data.frame", a data.frame with the following columns:
chr
The chromosome
pos
The position (1-based)
ref
The reference (consensus) nucleotide
var
The variant nucleotide
p.val
The (corrected) p-value
freq.var
The relative frequency of the SNV
sigma2.freq.var
The estimated variance of the frequency
n.tst.fw
The variant counts in the test experiment, forward strand
cov.tst.fw
The coverage in the test experiment, forward strand
n.tst.bw
The variant counts in the test experiment, backward strand
cov.tst.bw
The coverage in the test experiment, backward strand
n.ctrl.fw
The variant counts in the control experiment, forward strand
cov.ctrl.fw
The coverage in the control experiment, forward strand
n.ctrl.bw
The variant counts in the control experiment, backward strand
cov.ctrl.bw
The coverage in the control experiment, backward strand
raw.p.val
The raw p-value
If value = "VCF", this functions returns a VCF-class object with the following entries: FIXED:
REF
Reference allele in control sample. Note that deletions in the control sample will be reported like insertions, e.g. if the consensus of the control is A,- at positions 1 and 2 (relative to the reference) and the test was A,A, then this would be denoted as REF="A" and VAR="AA" with coordinate IRanges(1,2). This may cause ambiguities when the VCF object is written to text with writeVcf(), which discards the width of the coordinate, and this variant remains indistinguishable from an insertion to the _reference_ genome.
VAR
Variant allele in test sample
QUAL
-10*log10(raw.p.val)
INFO:
VF
Variant frequency. Variant allele frequency in the test minus variant allele frequency in the control.
VFV
Variant frequency variance. Variance of the variant frequency; can be thought of as confidence interval.
GENO (one column for test and one column for control):
FW
Forward allele count
BW
Backward allele count
DFW
Forward read depth
DBW
Backward read depth

Examples

Run this code
## 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))

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