seqdata_nvar: Generate sequence data for nsnp variants

In Struglab/RVS: Robust Variance Score (RVS) test for association of variants from next generation sequence data with binary traits using external controls

Description

It calls functions generate_seqdata_1var,seq_eg_freq,rbindlist to generate sequence data, return a list including expected genotype probability (exp_prob, leng=nsample), population fequency (pop_frq,leng=3),true genotype(geno),concatenated error rate(verror) and read depth(vrdepth)

Usage

seqdata_nvar(nsnp, ncase, ncont, mdcase, sddcase, mdcont, sddcont, mecase,
  sdecase, mecont, sdecont, mmafcase, mmafcont)

Arguments

nsnp,	number of variants (integer) >0
ncase,	number of cases (integer) >0
ncont,	number of controls (integer) >0
mdcase,	average read depth in cases (double) >0
sddcase,	standard deviation of read depth in cases (double) >0
mdcont,	average read depth in controls (double) >0
sddcont,	standard deviation of read depth in controls (double) >0
mecase,	average error rate, probability that sequence call is wrong (double) for case>0
sdecase,	standard deviation of error rate (double) for case >0
mecont,	average error rate, probability that sequence call is wrong (double) for cont >0
sdecont,	standard deviation of error rate (double) for cont >0
mmafcase,	a vector of MAF for nsnp variants in cases, HWE is assumed >0
mmafcont,	a vector of MAF for nsnp variants in controls

Value

a list including expected genotype probability (exp_prob, leng=nsample), population fequency (pop_frq,leng=3),true genotype(geno),and read depth(vrdepth), and ncase and ncont

Struglab/RVS documentation built on May 9, 2019, 3:11 p.m.