sumFREGAT (version 1.0.0)

MLR: Multiple Linear Regression

Description

Multiple linear regression approach on summary statistics

Usage

MLR(scoreFile, geneFile, regions, cor.path = "", annoType = "",
n, write.file = FALSE)

Arguments

scoreFile

name of data file generated by prep.score.files().

geneFile

name of a text file listing genes in refFlat format. If not set, hg19 file will be used (see Examples below).

regions

character vector of gene names to be analysed. If not set, function will attempt to analyse all genes listed in geneFile.

cor.path

path to a folder with correlation files (one file per each gene to be analysed). Names of correlation files should be constructed as "geneName.cor" (e.g. "ABCG1.cor", "ADAMTS1.cor", etc.) Each file should contain a square matrix with correlation coefficients (r) between genetic variants of a gene. An example of correlation file format: "snpname1" "snpname2" "snpname3" ... "snpname1" 1 0.018 -0.003 ... "snpname2" 0.018 1 0.081 ... "snpname3" -0.003 0.081 1 ... ... One way to generate such file from original genotypes is: write.table(cor(g), file = paste0(geneName, ".cor")) where g is a genotype matrix (nsample x nvariants) for a given gene with genotypes coded as 0, 1, 2 (exactly the same coding that was used to generate betas).

annoType

for files annotated with the seqminer package, a character (or character vector) indicating annotation types to be used (e.g. "Nonsynonymous", "Start_Loss", "Stop_loss", "Essential_Splice_Site")

n

size of the sample on which summary statitics were obtained.

write.file

output file name to write results as they come (sequential mode only).

...

other arguments that could be passed to null(), read.plink() and readVCFToMatrixByGene().

Value

A data frame containing P values, numbers of variants and filtered variants for each of analyzed regions.

Examples

# NOT RUN {
## Run MLR with example files:
VCFfileName <- system.file("testfiles/CFH.scores.anno.vcf.gz",
	package = "sumFREGAT")
cor.path <- system.file("testfiles/", package = "sumFREGAT")
n <- 85 # your sample size
out <- MLR(VCFfileName, region = 'CFH', cor.path = cor.path, n = n)

# }