FARVATX as of January 11, 2018
◎ Copyright (c) Sungkyoung Choi and Sungyoung Lee. All rights reserved.
1. Input file
1.1. Genotype data
: FARVATX support PLINK’s ped and binary format.
1.1.1 PED FILE
: The PED file is a white-space (tab or space) delimited file : the first six columns are mandatory:
1.1.2 MAP FILE
: Each line of the MAP file describes a single marker and must contain 4 columns:
1.2. Phenotype data
: Sample lines of phenotype and covariates file. (tab or space delimited)
1.3. Set file (gene-marker set)
: The name of the marker set file which defines Gene sets. The first column of the file must be Gene ID, and the second column must be Marker ID.
2. Create Kinship Coefficient Matrix
Make sure that ped and map (ped format) or bed, bim, and fam file (binary format) exist with the same prefix.
> farvatx --bed rare_test.bed --makecor --kinship --x2 (will generate res.theo.cor)
3. Run FARVATX
: with the ped/bed files, gene-marker set file, phenotype, and Kinship Coefficient Matrix as follows.
> farvatx --bed rare_test.bed --set test.group --genetest --cor res.theo.cor --genesummary --mispheno NA --out results_theo
4. Biological Model
: X chromosome inactivation (XCI) and escaped XCI (E-XCI) are efficiently tested with d = 0.5 and d = 1 respectively. Appropriate choices of d for Skewed XCI (S-XCI) toward either the normal and deleterious allele may be d = 0.25 and d = 0.75 respectively.
5. Output file
: This will generate the following files:
*[out_prefilx].gene.res : [CHR], [GENE], [NSAMP], [SZSET], [NVARIANT], [NSINGLETON],[MAC], [NIMP], [START], [END], [P_FARVAT_XB#], [P_FARVAT_XC#], [P_FARVAT_XO#], and [P_FARVAT_XD].
CHR: Chromosome Number
GENE: Gene name
NSAMP: The number of samples
SZSET: The number of variants from gene that existing in the dataset
NVARIANT: The number of variants (SNPs)
NSINGLETON: The number of singleton variants in current chromosome
MAC: The number of allele count
NIMP: The number of imputed genotype for the variant
START: Minimum position of variant belongs to gene
END: Maximum position of variant belongs to gene
P_FARVAT_XB0.25: p-value of FARVAT-XB under S-XCI to normal allele
P_FARVAT_XC0.25: p-value of FARVAT-XC under S-XCI to normal allele
P_FARVAT_XO0.25: p-value of FARVAT-XO under S-XCI to normal allele
P_FARVAT_XB0.5: p-value of FARVAT-XB under random XCI
P_FARVAT_XC0.5: p-value of FARVAT-XC under random XCI
P_FARVATX_XO0.5: p-value of FARVAT-XO under random XCI
P_FARVAT_XB0.75: p-value of FARVAT-XB under S-XCI to deleterious allele
P_FARVAT_XC0.75: p-value of FARVAT-XC under S-XCI to deleterious allele
P_FARVAT_XO0.75: p-value of FARVAT-XO under S-XCI to deleterious allele
P_FARVAT_XB1: p-value of FARVAT-XB under E-XCI
P_FARVAT_XC1: p-value of FARVAT-XC under E-XCI
P_FARVAT_XO1: p-value of FARVAT-XO under E-XCI
P_FARVAT_XD: p-value of FARVAT-XD