seq_eg_freq: use the simulated data to calculate the expected genotype...
In Struglab/RVS: Robust Variance Score (RVS) test for association of variants from next generation sequence data with binary traits using external controls
Description
Usage
Arguments
Value
Description
use the output of generate_seqdata_1var as input to calculate the expected genotype probability and population frequency
It calls subfunction calc_Mr and calc_EM for population frequency of P(G=AA,AB,BB),
It calls subfunction calc_pobs_ndepth, calc_EG_general and the populationfrequency for expected genotype probability
Usage
1
seq_eg_freq(vgeno, seq, verror, vrdepth)
Arguments
vgeno,
the concatenated true genotype for each sample
seq,
the concatenated sequence data
verror,
the concatenated error rate for each sequence data
vrdepth,
the concatenated error rate for each sample
Value
a list including expected genotype probability (exp_prob, leng=nsample), population fequency (pop_frq,leng=3),true genotype(geno),and read depth(vrdepth), two numerics for number of cases (ncase) and controls (ncont)
Struglab/RVS documentation built on May 9, 2019, 3:11 p.m.
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Description Usage Arguments Value
Description
use the output of generate_seqdata_1var as input to calculate the expected genotype probability and population frequency
It calls subfunction calc_Mr and calc_EM for population frequency of P(G=AA,AB,BB),
It calls subfunction calc_pobs_ndepth, calc_EG_general and the populationfrequency for expected genotype probability
Usage
1 | seq_eg_freq(vgeno, seq, verror, vrdepth)
|
Arguments
vgeno, |
the concatenated true genotype for each sample |
seq, |
the concatenated sequence data |
verror, |
the concatenated error rate for each sequence data |
vrdepth, |
the concatenated error rate for each sample |
Value
a list including expected genotype probability (exp_prob, leng=nsample), population fequency (pop_frq,leng=3),true genotype(geno),and read depth(vrdepth), two numerics for number of cases (ncase) and controls (ncont)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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