generate_seqdata_1var: Generate sequence data for ncase and ncontrol indiviudal at...

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

Description

Generate sequence data for ncase and ncontrol indiviudal at one loci it calls functions generate_seq_1ind to generate sequence data for ncase and ncont at one loci, read depth for two samples (case,cont) follow normal distribution of N(mdcase,sdcase) and N(mdcont, sdcont) respectively.

Usage

generate_seqdata_1var(ncase, ncont, mdcase, sddcase, mdcont, sddcont, mecase,
  sdecase, mecont, sdecont, mafcase, mafcont)

Arguments

ncase,	an integer to specify how many case samples
ncont,	an integer to specify how many control samples
mdcase,	the mean read depth for case
sddcase,	the stand variance of the read depth for case
mdcont,	the mean read depth for cont
sddcont,	the stand deviation of the read depth for cont
mecase,	the mean of error rate, probability that sequence call is wrong (double) for case>0
sdecase,	standard deviation of error rate (double) for case >0
mecont,	the mean of error rate, probability that sequence call is wrong (double) for cont >0
sdecont,	standard deviation of error rate (double) for cont >0
mafcase,	a numeric to specify the minor allele freq for the variant in case
mafcont,	a numeric to specify the minor allele freq for the variant in cont

Value

a list including four vectors: concatenated read depth for each individual (vrdepth, leng(vrdepth)=ncase+ncont), error rate of each sequence for each sample (verror, leng(verror)=sum(vrdepth)), the sequencing data (seq, leng=leng(verror)) and true genotype data (vgeno,leng=leng(vrdepth)),

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