Description Usage Arguments Value
This function calculates a likelihood matrix P(D|G) given a vector of error rates and a vector of sequence reads, where D is the sequencing data and G is the true genotype. It uses function calc_psingle
to calculate the likelihood for each read given one possible genotype (AA, Aa or aa).
It is a more general case of calc_pobs_ndepth
with an additional param rdv, and called from generate_seqdata
.
1 | calc_Mr(error, vect_row_reads, ndepth = 1, rdv)
|
error |
vector of base call error rates; Uses the same error input in the |
vect_row_reads |
row vector of sequence reads consisting of 'A','G','T' or 'C', same as output from function |
ndepth |
read depth (integer), it eaquals to the length of error or vect_row_reads, or sum of vector rdv |
rdv |
integer vector of read depths concatenated for all samples. |
a matrix (M) with 3 columns representing P(read|AA), P(read|Aa) and P(read|aa), where row dimensions equal length(error)=length(vect_row_reads).
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