SHLR (version 1.0)

run.SHLR.scan:

SHLR scan

Description

This is a wrapper function that performs SHLR or SHLR-fam statistic to a genomic region one marker at a time. The scan results will be outputted to a file.

Usage

run.SHLR.scan(haps, phen, marker.map, outfile, outcome, 
out.dist = "Gaussian", cov = "", missing.id.code = "0", 
method, nSplits = 1, pca.thres = NULL, hap.freq.thres = 0.005, 
window.size = 100, threads = NULL, corstr = "kinship", 
std.err = "naive", gender = "", fid = "", iid = "", pid = "", 
mid = "")

Arguments

haps

Haplotypes array stored as a string of character per row. Every two rows contains the haplotypes for each individual. (Required)

phen

Phenotype table. The phenotype table contains information about trait of interest and other covariates. (Required)

marker.map

The marker map contains information about marker name (1st column) and marker position (2nd column). (Required)

outfile

The desired name of the output file. (Required)

outcome

The column name for the phenotype of interest in the phenotype table. (Required)

out.dist

The assumed outcome distribution of the model. e.g. : gaussian, binomial, etc. (Required)

cov

The column names for the covariates in the phenotype table.

missing.id.code

The code for missing id in the pedigree structure. Usually, it is coded as '0'. (Required only if method is 'SHLR-fam' and corstr is 'kinship')

method

The choice for the SHLR method (i.e. : SHLR or SHLR-fam). (Required)

nSplits

The number of splits. This option will determine how often the program prints out results to the output file.

pca.thres

The proportion of variation retained in the design matrix of the model based on PCA.

hap.freq.thres

The minimum haplotype frequency proportion threshold. Haplotypes that meet this threshold will be considered in the model.

window.size

The number of markers that form the haplotype.

threads

The number of CPUs for parallel computation.

corstr

The type of correlation structure. The options are: 'kinship', 'exchangeable', or 'independence'. (SHLR-fam parameter)

std.err

The method for estimating variance for SHLR-fam. The options are: 'naive' or 'sandwich'. (SHLR-fam parameter)

gender

The column name that indicates gender in the phenotype table. (Required if method is SHLR-fam and cor.str is 'kinship')

fid

The column name that indicates family id in the phenotype table. (Required if method is SHLR-fam and cor.str is 'kinship')

iid

The column name that indicates individual id in the phenotype table. (Required if method is SHLR-fam and cor.str is 'kinship')

pid

The column name that indicates father id in the phenotype table. (Required if method is SHLR-fam and cor.str is 'kinship')

mid

The column name that indicates mother id in the phenotype table. (Required if method is SHLR-fam and cor.str is 'kinship')

Examples

library(SHLR)

####reading in pedigree data
fam <- read.table(system.file("extdata","plink.fam",package="SHLR"), 
    header=FALSE, stringsAsFactors=FALSE)
colnames(fam) <- c("fam_id","id","dad_id","mom_id","sex","qtrait")

####add simulated covariates to create phenotype table
N <- dim(fam)[1]
cov1 <- rnorm(N, 0, 2)
cov2 <- rbinom(N, 1, 0.7)
phen <- data.frame(fam, cov1=cov1, cov2=cov2)

##Read phased haplotype
shapeit <- read.shapeit.haps(system.file("extdata","phased.haps",package="SHLR"))
haps <- shapeit$haps
marker.map <- shapeit$marker.map

##Initialize parameters for SHLR.scan
outfile <- "out.txt"
outcome <- "qtrait"
cov <- c("sex","cov1","cov2")
famid <- "fam_id"
iid <- "id"
pid <- "dad_id"
mid <- "mom_id"
gender <- "sex"
missid <- "0"
corstr <- "kinship"
out_dist <- "gaussian"
std.err <- "naive"
method <- "SHLR-fam"
window.size <- 35
pca.thres <- 0.8
nSplits <- 1

run.SHLR.scan(haps, phen, marker.map, outfile,
        outcome, out.dist=out_dist, cov=cov, missing.id.code=missid,
        method=method, nSplits=nSplits, pca.thres=pca.thres, hap.freq.thres=0.001,
        window.size=window.size, threads=2, corstr=corstr,
        std.err=std.err, gender=gender, fid=famid, iid=iid, pid=pid, mid=mid)