compIdent: Construct identity snp comparison plot

Description

Given the bam file path, count the number of reads at the 24 SNP locations

Usage

compIdent(x, genome, target = NULL, debug = FALSE, mainLayer = NULL, covLayer = NULL, out = "plot")

Arguments

data frame with rows representing samples and column names "sample_name", "bamfile". Columns should correspond to a sample name and a bam file path.

genome

Object of class BSgenome specifying the genome.

target

Object of class data frame containing target locations in 1-base format and containing columns names "chr", "start", "end", "var", "name". Columns should correspond to chromosome, start, end, variant allele, name of location.

debug

Boolean specifying if test datasets should be used for debugging.

mainLayer

Valid ggplot2 layer for altering the main plot.

covLayer

Valid ggplot2 layer for altering the coverage plot.

out

Character vector specifying the the object to output, one of "data", "grob", or "plot", defaults to "plot" (see returns).

Value

One of the following, a list of dataframes containing data to be plotted, a grob object, or a plot.

Details

compIdent is a function designed to comppare samples via variant allele frequencies (VAF) at specific sites. By default these sites correspond to 24 identity snps originating from the hg19 assembly however the user can specify alternate sites via the target paramter. To view the 24 identity snp locations use GenVisR::SNPloci.

Samples from the same origin are expected to have similar VAF values however results can skew based on copy number alterations (CNA). The user is expected to ensure no CNA occur at the 24 identity snp sites.

For display and debugging purposes a debug parameter is available which will use predefined data instead of reading in bam files. Note that data in the debug parameter is only available at the afore mentioned 24 sites.

Examples

Run this code

# Read in BSgenome object (hg19)
library(BSgenome.Hsapiens.UCSC.hg19)
hg19 <- BSgenome.Hsapiens.UCSC.hg19

# Generate plot
compIdent(genome=hg19, debug=TRUE)