mymae {poolHelper}

Average absolute difference between allele frequencies computed from genotypes supplied by the user and from Pool-seq data

Description

Calculates the average absolute difference between the allele frequencies computed directly from genotypes and from pooled sequencing data. The genotypes used should be supplied by the user and can be simulated using different software and under the demographic model of choice.

Usage

mymae(
  genotypes,
  pools,
  pError,
  sError,
  mCov,
  vCov,
  min.minor,
  minimum = NA,
  maximum = NA
)

Arguments

genotypes

a list of genotypes, where each entry is a matrix corresponding to a different locus. At each matrix, each column is a different SNP and each row is a different individual. Genotypes should be coded as 0, 1 or 2.

pools

a list with a vector containing the size (in number of diploid individuals) of each pool. Thus, if a population was sequenced using a single pool, the vector should contain only one entry. If a population was sequenced using two pools, each with 10 individuals, this vector should contain two entries and both will be 10.

pError

an integer representing the value of the error associated with DNA pooling. This value is related with the unequal contribution of both individuals and pools towards the total number of reads observed for a given population - the higher the value the more unequal are the individual and pool contributions.

sError

a numeric value with error rate associated with the sequencing and mapping process. This error rate is assumed to be symmetric: error(reference -> alternative) = error(alternative -> reference). This number should be between 0 and 1.

mCov

an integer that defines the mean depth of coverage to simulate. Please note that this represents the mean coverage across all sites.

vCov

an integer that defines the variance of the depth of coverage across all sites.

min.minor

is an integer representing the minimum allowed number of minor-allele reads. Sites that, across all populations, have less minor-allele reads than this threshold will be removed from the data.

minimum

an optional integer representing the minimum coverage allowed. Sites where the population has a depth of coverage below this threshold are removed from the data.

maximum

an optional integer representing the maximum coverage allowed. Sites where the population has a depth of coverage above this threshold are removed from the data.

Details

The average absolute difference is computed with the mae function, assuming the frequencies computed directly from the genotypes as the actual input argument and the frequencies from pooled data as the predicted input argument.

Note that this functions allows for different combinations of parameters. Thus, the effect of different combinations of parameters on the average absolute difference can be tested. For instance, it is possible to check what is the effect of different coverages by including more than one value in the mCov input argument. This function will run and compute the average absolute difference for all combinations of the pools, pError and mCov input arguments.

Value

a data.frame with columns detailing the number of diploid individuals, the pool error, the number of pools, the number of individuals per pool, the mean coverage, the variance of the coverage and the average absolute difference between the frequencies computed from genotypes and from pooled data.

Examples

# 100 individuals sampled at a single locus
genotypes <- run_scrm(nDip = 100, nloci = 1, theta = 5)
# compute the mean absolute error assuming a coverage of 100x and two pools of 50 individuals each
mymae(genotypes = genotypes, pools = list(c(50, 50)), pError = 100, sError = 0.001,
mCov = 100, vCov = 250, min.minor = 0)

# 10 individuals sampled at 5 different loci
genotypes <- run_scrm(nDip = 10, nloci = 5, theta = 5)
# compute the mean absolute error assuming a coverage of 100x and one pool of 10 individuals
mymae(genotypes = genotypes, pools = list(10), pError = 100, sError = 0.001,
mCov = 100, vCov = 250, min.minor = 0)