ldsc: LD score regression

Description

The ldsc function is used for LDSC analysis

Usage

ldsc(
  Glist = NULL,
  ldscores = NULL,
  sets = NULL,
  method = "regression",
  residual = FALSE,
  z = NULL,
  b = NULL,
  seb = NULL,
  af = NULL,
  stat = NULL,
  tol = 1e-08,
  n = NULL,
  intercept = TRUE,
  what = "h2",
  maxZ2 = NULL,
  SE.h2 = FALSE,
  SE.rg = FALSE,
  blk = 200
)

Value

Returns a matrix of heritability estimates when what="h2", and if SE.h2=TRUE standard errors (SE) and significance levels (P) are returned. If what="rg" an n-by-n matrix of correlations is returned where the diagonal elements being h2 estimates. If SE.rg=TRUE a list is returned with n-by-n matrices of genetic correlations, estimated standard errors and significance levels.

Arguments

Glist: list of information about genotype matrix stored on disk
ldscores: vector of LD scores (optional as LD scores are stored within Glist)
sets: Optional list specifying sets of SNPs for mapping.
method: the regression method to use, options include "regression", "bayesC", "bayesR".
residual: logical if TRUE then add a residual that capture the h2 not explained by the sets
z: matrix of z statistics for n traits
b: matrix of marker effects for n traits if z matrix not is given
seb: matrix of standard errors of marker effects for n traits if z matrix not is given
af: vector of allele frequencies
stat: dataframe with marker summary statistics
tol: smallest value for h2
n: vector of sample sizes for the traits (element i corresponds to column vector i in z matrix)
intercept: logical if TRUE the LD score regression includes intercept
what: either computation of heritability (what="h2") or genetic correlation between traits (what="rg")
maxZ2: maximum value for squared value of z-statistics
SE.h2: logical if TRUE standard errors and significance for the heritability estimates are computed using a block jackknife approach
SE.rg: logical if TRUE standard errors and significance for the genetic correlations are computed using a block jackknife approach
blk: numeric size of the blocks used in the jackknife estimation of standard error (default = 200)

Author

Peter Soerensen

Palle Duun Rohde

Examples

Run this code



# Plink bed/bim/fam files
 #bedfiles <- system.file("extdata", paste0("sample_chr",1:2,".bed"), package = "qgg")
 #bimfiles <- system.file("extdata", paste0("sample_chr",1:2,".bim"), package = "qgg")
 #famfiles <- system.file("extdata", paste0("sample_chr",1:2,".fam"), package = "qgg")
 #
 ## Summarize bed/bim/fam files
 #Glist <- gprep(study="Example", bedfiles=bedfiles, bimfiles=bimfiles, famfiles=famfiles)

 #
 ## Filter rsids based on MAF, missingness, HWE
 #rsids <-  gfilter(Glist = Glist, excludeMAF=0.05, excludeMISS=0.05, excludeHWE=1e-12) 
 #
 ## Compute sparse LD (msize=size of LD window)
 ##ldfiles <- system.file("extdata", paste0("sample_chr",1:2,".ld"), package = "qgg")
 ##Glist <- gprep(Glist, task="sparseld", msize=200, rsids=rsids, ldfiles=ldfiles, overwrite=TRUE)
 #
 #
 ##Simulate data
 #W1 <- getG(Glist, chr=1, scale=TRUE)
 #W2 <- getG(Glist, chr=2, scale=TRUE)

 #W <- cbind(W1,W2)
 #causal <- sample(1:ncol(W),5)

 #b1 <- rnorm(length(causal))
 #b2 <- rnorm(length(causal))
 #y1 <- W[, causal]%*%b1 + rnorm(nrow(W))
 #y2 <- W[, causal]%*%b2 + rnorm(nrow(W))

 #data1 <- data.frame(y = y1, mu = 1)
 #data2 <- data.frame(y = y2, mu = 1)
 #X1 <- model.matrix(y ~ 0 + mu, data = data1)
 #X2 <- model.matrix(y ~ 0 + mu, data = data2)

 ## Linear model analyses and single marker association test
 #maLM1 <- lma(y=y1, X=X1,W = W)
 #maLM2 <- lma(y=y2,X=X2,W = W)
 #
 ## Compute heritability and genetic correlations for trait 1 and 2
 #z1 <- maLM1[,"stat"]
 #z2 <- maLM2[,"stat"]

 #z <- cbind(z1=z1,z2=z2)

 #h2 <- ldsc(Glist, z=z, n=c(500,500), what="h2")
 #rg <- ldsc(Glist, z=z, n=c(500,500), what="rg")