Checks if the reference character of the major allele is the same in all populations present in the dataset.
checkMajor(nPops, major, minor, rMajor, rMinor)a list with four named entries:
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.
Each of those matrices is similar to the corresponding input but with the major and minor allele switched when appropriate.
is an integer indicating the total number of different populations in the dataset.
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.
When working with two populations, the reference character of the major allele is compared between the two populations. If they are not the same, this function switches the major and minor reference character of the second population i.e. the original reference character of the major allele of the second population is now the reference character of the minor allele of the second population. It also switches the number of reads so that the number of major-allele reads is now the number of minor-allele reads and vice-versa. When working with four populations, and if the major reference character is not the same at all populations, this function checks if any of the reference characters appears in three populations. If it does, then the major and minor reference character and reads are switched in the remaining population. If not, then the reference character and reads of two random populations are switched.
Finally, for both datasets with two or four populations, this function checks if the total number of major-allele reads, across all populations and after the switch, is larger than the total number of minor-allele reads. If this is not true, then we switch the major and minor allele so that the more frequent one corresponds to the major allele.