RareVariantVis (version 1.6.2)

chromosomeVis: Visualization of variants on the chromosome

Description

Reads file containing table of variants (or alternatively, vcf file) from one chromosome and provides adequate visualization. Function outputs visualization png figure in current working directory. Figure illustrates variants (dots) in their genomic coordinates (x axis). Ratio of alternative reads and depth (y axis) gives information about type of variant: homozygous alternative (expected ratio 1) and heterozygous (expected ratio 0.5). Green dots represent rare variants that pass filters: coding/UTR, nonsynonymous variant with dbSNP frequency < 0.01. Orange vertical lines depict position of centromere. Red curve illustrates moving average of alternative reads/depth ratio. High values of this curve (exceedint 0.75) can suggest potential homozygous/deleterious regions. In addition, file containing table with rare variants only is generated. Table includes the same columns as input file.

Usage

chromosomeVis(file, sampleName, chromosome, centromeres, pngWidth,
pngHeight, plot, frFilter, dpFilter, vcf, posFilter)

Arguments

file

a connection or a character string giving the name of the text file/vcf to load. File should include following information: Start.position - for location on chromosome, SNP.Frequency - for dbSNP frequency, DP - sequencing depth, AD - allelic depths for reference and alternative alleles, Gene.name - gene symbol, Gene.component and Variant.type. Example of the table is provided in attached SonVariantsChr21.txt file. Example file can be loaded using command data(SonVariantsChr21) from library AshkenazimSonChr21.

sampleName

character string giving the sample name

chromosome

a numeric value giving the analyzed chromosome number

centromeres

a data frame providing location of centromeres on chromosomes

pngWidth

a numeric value setting width of output figure

pngHeight

a numeric value setting height of output figure

plot

logic value indicating if plot should be displayed or saved on the current working directory

frFilter

numeric value indicating dbSNP frequency filtering threshold (default 0.01). It is recommended not to change this value in the first phase of experiments.

dpFilter

numeric value indicating DP filtering threshold (default 10). It is recommended not to change this value in the first phase of experiments.

vcf

logic value indicating if input file is in vcf format. Vcf is supported, however data frame inputs are recommended.

posFilter

vector of values indicating positions of variants to be filtered out in addition to other filtering settings (default 0). Could be used for external database or in-house database filtering.

Value

comp1

function returns html file with visualization and txt file with rare variants

Examples

## example data
library(AshkenazimSonChr21)

## example of data frame input
chromosomeVis(SonVariantsChr21, "1", 21, CentromeresHg19, 1600, 1200)

## example of vcf file input
fl <- system.file("extdata", "SonVariantsChr21.vcf.gz", package="AshkenazimSonChr21")
chromosomeVis(fl, "1", 21, CentromeresHg19, 1600, 1200, vcf = TRUE)