Package index • GXwasR

All functions

AncestryCheck(): AncestryCheck: Evaluation of the samples' ancestry label.

ClumpLD(): ClumpLD: Clumping SNPs using linkage disequilibrium between SNPs

ComputeGeneticPC(): ComputeGeneticPC: Computing principal components from genetic relationship matrix

ComputeLD(): ComputeLD: Compute Linkage Disequilibrium (LD) for SNP Data

ComputePRS(): ComputePRS: Computing polygenic risk score (PRS)

DiffZeroOne(): DiffZeroOne: Assessing the Z-score for deviation from one and zero.

DummyCovar(): DummyCovar: Recode a categorical variable to a set of binary dummy variables.

EstimateHerit(): EstimateHerit: Computing SNP heritability i.e., the proportion of phenotypic variance explained by SNPs.

Example_covarfile: Example of covariate dataframe

Example_h2data: Example dataset for h2 estimation between male and female for eight different traits

Example_phenofile: Example dataset for phenotype file

Example_pthresoldfile: Example dataset with p-value threshold

Example_rgdata: Example dataset for running DiffZerOne function

Ffile: Example dataset for FemaleWAS

FilterAllele(): FilterAllele: Filtering out the multi-allelic variants

FilterPlinkSample(): FilterPlinkSample: Making PLINK files with desired samples.

FilterRegion(): FilterRegion: Filter chromosomal regions.

FilterSNP(): FilterSNP: Filter out SNPs.

GXWASmiami(): Miami plot

GXwas(): GXwas: Running genome-wide association study (GWAS) and X-chromosome-wide association study (XWAS) models.

GXwasR_data(): GXwasR Data

GeneticCorrBT(): GeneticCorrBT: Computing genetic correlation between two traits.

GetMFPlink(): GetMFPlink: Getting male and female PLINK binary files.

LDPrune(): LDPrune: Performs LD pruning on SNP data using PLINK

MAFdiffSexControl(): MAFdiffSexControl: Test for significantly different minor allele frequency (MAF) between sexes in control samples

MergeRegion(): MergeRegion: Merging two sets of PLINK binary files.

MetaGWAS(): MetaGWAS: Combining summary-level results from two or more GWA studies into a single estimate.

Mfile: Example dataset for MaleWAS

PlinkSummary(): PlinkSummary: Summary of PLINK format genotype dataset

PvalComb(): PvalComb

QCsample(): QCsample: Quality control for samples in the PLINK binary files.

QCsnp(): QCsnp: Quality control (QC) for SNPs.

Regression_Ex: Example dataset for regression

SexCheck(): SexCheck: Compare sex assignments in the input PLINK files with those imputed from X chromosome inbreeding coefficients

SexDiff(): SexDiff: Sex difference in effect size for each SNP using t-test.

SexDiffZscore(): SexDiffZscore: Z-score-based sex difference test.

SexRegress(): SexRegress: Performing linear regression analysis with quantitative response variable.

Summary_Stat_Ex1: Example dataset for GWAS summary statistics

Summary_Stat_Ex2: Example dataset for GWAS summary statistics

SumstatGenCorr(): SumstatGenCorr: Genetic Correlation Calculation from GWAS Summary Statistics

TestXGene(): TestXGene: Performing gene-based association test using GWAS/XWAS summary statistics.

XWAS_Summary_Example: Example dataset for XWAS summary statistics

Xhwe(): Xhwe: Filter X-chromosome variants for HWE in females.

example_data_study_sample_ancestry: Example of ancestry dataframe of samples

executePlinkMAF(): executePlinkMAF: Execute PLINK to Calculate Minor Allele Frequencies (MAF)

highLD_hg19: Example dataset for high LD regions in hg19 built

plinkVCF(): plinkVCF: Converting VCF files to PLINK binary files and vice-versa.

validate_reference_data(): Validate Path to Reference Data Set