detect_allele_problems: Detect alternate allele problems

In thierrygosselin/radiator: RADseq Data Exploration, Manipulation and Visualization using R

Detect alternate allele problems

Description

Detect alternate allele problems. Used internally in radiator and might be of interest for users. The function computes alternate allele counts and looks for alternate alleles bellow a certain threshold. The summary statistics for the markers with problematic allele is computed based on coverage and genotype likelihood. This function is very fast to highlight: i) bias in representation of allelic copies and unequal coverage and ii) type I error during genotyping of heterozygote with low coverage data.

Usage

detect_allele_problems(data, allele.threshold = 3, verbose = TRUE, ...)

Arguments

data	A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into radiator tidy_genomic_data.
allele.threshold	(integer) Threshold of alternate allele copies. Below this threshold markers are blacklisted. Choose this threshold based on your tolerance for uninformative or unreliable information and minor allele frequency. Summary statistics for this blacklist will be calculated. See details for more info.
verbose	(optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.
...	(optional) Advance mode that allows to pass further arguments for fine-tuning the function (see details).

Details

Under developement, use with caution

Input files: see radiator tidy_genomic_data for detailed information about supported file format.

allele.threshold:

An allele.threshold = 1, says that you want to check the statistics for markers with only 1 copy of the alternate allele. Said differently, allele.threshold = 1 = only 1 heterozygote individual is making this marker polymorphic, very thin line if this allele is backed by less than 3 reads.

Similarly, a allele.threshold = 2 can represent markers with 2 heterozygote individuals calling the polymorphic markers or 1 individual homozygote for the alternate allele.

Look for problem with :

• read depth/coverage problem

• high imbalance between the alt and ref depth coverage

• genotype likelihood abnormally lower than normal

• alternate allele with NA for read depth information

Alternate allele with no depth information: You can highlight those problematic genotypes with alt.no.depth <- dplyr::filter(your.object$allele.summary, is.na(ALLELE_ALT_DEPTH))

Use the summary statistics of the blacklisted markers to refine update the blacklist of markers. You can decide to discard the markers or blacklist the problematic genotypes. radiator tidy_genomic_data and genomic_converter allows to erase problematic genotypes using a blacklist of genotypes...

Value

A list with summary, plot and blacklist. Summary statistics for the blacklisted markers are generated and include coverage and genotype likelihood information.

$alt.allele.count.plot: Distribution of marker's alternate allele number. The shape is usually skewed right.

$alt.depth.count.distribution.plot: Distribution of markers alternate allele depth (in number of read). The range showed on the plot is between 1 and 10, and you decide your tolerance for low coverage and good genotype calls.

This plot is associated with $number.markers, a table that shows the number of markers <= allele.threshold . Also in the table, the range of alternate allele read depth (1 to 10), same as plot but showing here the the cumulative number of markers. Again, would you trust a marker with only 1 alternate allele (an heterozygote individual) with a read depth of 1 or 2 ?

Author(s)

Thierry Gosselin [e-mail]

Examples

## Not run: 
problem <- detect_allele_problems(
        data = salamander,
        strata = "strata.salmon.tsv",
        allele.threshold = 3)

# The default with this function:
# filter.monomorphic = TRUE # = discarded
# filter.common.markers = TRUE # markers not in common between pop are discarded

## End(Not run)

thierrygosselin/radiator documentation built on April 25, 2024, 3:20 a.m.