prep.score.files {sumFREGAT}

Prepare score files

Description

Calculates Z scores from P values and beta input

Usage

prep.score.files(data, reference = "ref1KG.MAC5.EUR_AF.RData",
output.file.prefix)

Arguments

data

a file name or data.frame with two mandatory columns (case-insensitive header):

"ID": unique names of genetic variants (rsIDs if 1000G correlation matrices will be used)
"P": P value

Chromosome and positions are desirable:

"CHROM": chromosome
"POS": positions for the same build as in gene.file (see gene-based test functions)

Map data are required to assign genetic variants to genes. If not present in input file, the function will attempt to link them from the reference file (see reference below).

Additional columns that can be present in input file to be used in gene-based tests:

"EA": effect allele
"BETA": effect size (betas and genetic correlations should be calculated for the same genotype coding)
"EAF": effect allele frequency

Effect allele and size data can be proccesed with reference file only (see reference below).

"REF": reference allele
"ALT": alternative allele

"REF" and "ALT" columns can be used to compare alleles with those in reference file and exclude genetic variants if alleles do not match

Annotation columns:

"ANNO": functional annotations (like "intron_variant", "synonymous", "missense" etc.)
"PROB", "PROB1", "PROB2", "PROB3" etc.: probabilities of a variant to be causal, can be passed to sumSTAAR() (PHRED scale) or FFGAS()

For example:

CHROM POS ID EA P BETA EAF
1 196632134 1:196632134 T 0.80675 0.22946 0.00588
1 196632386 1:196632386 A 0.48694 0.65208 0.00588
1 196632470 1:196632470 G 0.25594 -0.19280 0.19412

Avoid rounding of betas and P values as this can affect the precision of regional tests.

The more data (columns) is present in input file, the more gene-based tests are available to run. ACAT test is available with minimal input (rsIDs and P values). Together with correlation matrices (reference matrices calculated from 1000G data are available at http://mga.bionet.nsc.ru/sumFREGAT/) it allows to run minp(), simpleM, and sumchi() tests. Adding info on effect allele ("EA") and effect size ("BETA") enables essentially all sumFREGAT tests. Adding allele frequencies enables standard weighting via beta distribution (see gene-based test functions for details).

reference

path to a reference file or data.frame with additional data needed to recode user data according to correlation matrices that will be used. Reference file for 1000G correlation matrices is available at http://mga.bionet.nsc.ru/sumFREGAT/. Reference file contains "ID" column with names of genetic variants that are used in correlation matrices as well as "REF" and "ALT" columns with alleles that were coded during calculation of correlation coefficients as 0 and 1, respectively. Effect sizes from data will be inverted for variants with effect alleles different from "ALT" alleles in reference data. If presented, "REF" and "ALT" columns from the input data will be used to sort out variants with alleles different from those in reference data. The reference file can also be a source of map data and allele frequencies if they are not present in data. "AF" column in the reference file represents the allele frequency of "ALT" allele.

output.file.prefix

if not set, the input file name will be used as output prefix.

Value

does not return any value, writes output files with Z scores to be used in any type of gene-based analysis in sumFREGAT (see gene-based test functions).

Examples

## Not run: 

data <- system.file("testfiles/CFH.dat", package = "sumFREGAT")
prep.score.files(data, output.file.prefix = "CFH")

# requires reference file "ref1KG.MAC5.EUR_AF.RData" (can be downloaded
# at http://mga.bionet.nsc.ru/sumFREGAT/)

data <- system.file("testfiles/CFH.full.input.dat", package = "sumFREGAT")
prep.score.files(data, reference = "ref1KG.MAC5.EUR_AF.RData",
	output.file.prefix = "CFH.full")

data <- system.file("testfiles/CFH.prob.dat", package = "sumFREGAT")
prep.score.files(data, reference = "ref1KG.MAC5.EUR_AF.RData",
	output.file.prefix = "CFH.prob")

## End(Not run)