This functions checks if the sum of the number of major and minor allele reads of a given population is equal to the total depth of coverage of that population.
checkCoverage(nPops, info, major, minor, rMajor, rMinor, coverage)a list with the following elements:
a matrix with the general information about the dataset. Each row of this matrix corresponds to a different site.
a matrix with the reference character of the major allele. Each column of this matrix corresponds to a different population and each row to a different site.
a matrix with the reference character of the minor allele. Each column of this matrix corresponds to a different population and each row to a different site.
a matrix with the number of major-allele reads. Each row of this matrix is a different site and each column a different population.
a matrix with the number of minor-allele reads. Each row of this matrix is a different site and each column a different population.
a matrix with the total coverage. Each row of this matrix is a different site and each column a different population.
Each of those matrices is similar to the corresponding input but without any sites where the total depth of coverage does not match the sum of the major and minor allele reads.
is an integer indicating the total number of different populations in the dataset.
is a matrix containing information about the dataset. This matrix might contain several columns including one with the reference contig (chromosome), the position of the SNP in the reference contig and the reference character of the SNP. Note that each row of the matrix should be a different SNP and each column a different type of information.
is a matrix with the reference character of the major allele. Each column of the matrix should be a different population and each row a different SNP.
is a matrix with the reference character of the minor allele. Each column of the matrix should be a different population and each row a different SNP.
is a matrix with the number of major allele reads. Each column of the matrix should be a different population and each row a different SNP.
is a matrix with the number of minor allele reads. Each column of the matrix should be a different population and each row a different SNP.
is a matrix with the total number of reads i.e. the depth of coverage. Each column of the matrix should be a different population and each row a different SNP.
This verification is performed for all the populations included in the dataset. Any site where this verification fails for any of the populations is removed from the dataset. More precisely, if the sum of the number of major and minor allele reads of one population is not equal to the coverage of that population, then that site is removed from the data for all the populations.