summary-methods: Summary of a deepSNV object

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

Summary of a deepSNV object

Description

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

Usage

## S4 method for signature 'deepSNV'
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

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.