| compute_H1 {poolfstat} | R Documentation |
compute_H1
Description
Compute (uncorrected) 1-Q1 for each block-jackknife block (if any) and over all the SNPs (i.e., either within or outside blocks)
Usage
.compute_H1(refcount, totcount, nblocks, block_id, verbose)
Arguments
refcount |
Matrix of nsnpxnpop with counts (genotype or reads) for the reference allele |
totcount |
Matrix of nsnpxnpop with total counts or read coverages |
nblocks |
Integer giving the number of block-jackknife blocs (may be 0 if no block-jackknife) |
block_id |
Integer vector of length nsnps with the (0-indexed) id of the block to which each SNP belongs (-1 for SNPs outside blocks) |
verbose |
Logical (if TRUE progression bar is printed on the terminal) |
Details
Compute all the (uncorrected) H1=1-Q1 for each block-jackknife block (if any) and overall SNPs (within or outside blocks). It is indeed more convenient to compute H1 (rather than Q1) to apply corrections afterwards within R function
Value
Return a matrix with npops rows and nblocks+1 column giving the mean H1 of each pop within each block and for all SNPs (last column)
Examples
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