summary-methods: Summary of a deepSNV object

Description Usage Arguments Value Author(s) Examples

Description

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

Summary for deepSNV object

Usage

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## 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

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## 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))

mg14/deepSNV-old documentation built on May 22, 2019, 8:52 p.m.