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.
detect_allele_problems(data, allele.threshold = 3, verbose = TRUE, ...)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.
(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.
(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).
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 $number.markers, a table that shows the
number of markers <= allele.threshold . Also in the table, the
range of alternate allele read depth (1 to 10), same as plot but showing here
the the cumulative number of markers. Again, would you trust a marker with only
1 alternate allele (an heterozygote individual) with a read depth of 1 or 2 ?
Under developement, use with caution
Input files: see radiator tidy_genomic_data
for detailed information about supported file format.
allele.threshold:
An allele.threshold = 1, says that you want to check the statistics
for markers with only 1 copy of the alternate allele. Said differently,
allele.threshold = 1 = only 1 heterozygote individual is making this
marker polymorphic, very thin line if this allele is backed by less than 3 reads.
Similarly, a allele.threshold = 2 can represent markers with
2 heterozygote individuals calling the polymorphic markers or 1 individual
homozygote for the alternate allele.
Look for problem with :
read depth/coverage problem
high imbalance between the alt and ref depth coverage
genotype likelihood abnormally lower than normal
alternate allele with NA for read depth information
Alternate allele with no depth information: You can highlight those problematic genotypes with alt.no.depth <- dplyr::filter(your.object$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...
if (FALSE) { # \dontrun{
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
} # }