JAMexpanded.multi: Expanded version of JAM (a single-trait fine-mapping...

Description Usage Arguments Value Author(s)

View source: R/prep.R

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

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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

Author(s)

Jenn Asimit


jennasimit/flashfm documentation built on Aug. 9, 2021, 7:36 a.m.