JAMexpanded.multi: Expanded version of JAM (a single-trait fine-mapping...
In jennasimit/flashfm: flexible and shared information fine-mapping

JAMexpanded.multi

R Documentation

Expanded version of JAM (a single-trait fine-mapping approach) that first runs on thinned SNPs and then expands models on tag SNPs; this can run independently on multiple traits

Description

Expanded version of JAM (a single-trait fine-mapping approach) that first runs on thinned SNPs and then expands models on tag SNPs; this can run independently on multiple traits

Usage

JAMexpanded.multi(
  beta1,
  Gmat,
  snpinfo,
  ybar,
  Vy,
  N,
  chr = 10,
  fstub,
  mafthr = 0.005,
  path2plink,
  r2 = 0.99,
  save.path,
  related = FALSE,
  y = NULL
)

Arguments

`beta1`	list where each component is a named vector
`Gmat`	genotype matrix (reference or from sample) where SNPs are columns, indivudals are rows
`snpinfo`	a data.frame with columns: snpid, BP, allele1, allele2; BP is base pair position, allele1 is reference allele
`ybar`	vector of trait means; if related samples, this should be based on unrelated samples; if traits are transformed to be standard Normal, could set ybar as 0-vector
`Vy`	vector of trait variances; if related samples, this should be based on unrelated samples; if traits are transformed to be standard Normal, could set Vy as 1-vector
`N`	vector of sample sizes for each trait; if related samples then give effective sample sizes
`chr`	chromosome number
`fstub`	file stub for path with file prefix to save intermediate files (plink format and tag snp list)
`mafthr`	MAF threshold for filtering SNPs to include in fine-mapping; default is 0, assuming pre-filterec
`path2plink`	file path to plink
`r2`	r.squared threshold for thinning SNPs before JAM
`save.path`	path to save JAM output files; tmp files and could delete these later
`related`	logical indicating if samples are related (TRUE) or not (FALSE); default is FALSE
`y`	if available, matrix of trait measurements or indicators of non-NA trait measurements (columns are traits); used to get joint sample counts; default is NULL and if not provided an approximation is used based on vector of trait sample sizes

Value

list with 3 components: SM a list of snpmod objects giving fine-mapping results for each trait; mbeta a list of joint effect estimates for each trait; nsnps number of SNPs