FARVATX beta as of June 28, 2016

◎ Copyright (c) Sungkyoung Choi and Sungyoung Lee. All rights reserved.

The current version of FARVATX release is beta version. A complete version of the software will be appearing soon.



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)




: with the ped/bed files, gene-marker set file, phenotype, and Kinship Coefficient Matrix as follows.

farvatx --bed rare_test.bed --set --genetest --cor res.theo.cor --genesummary --mispheno -9 --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], [NVARIANT], [MAC], [P_FARVAT_XB#], [P_FARVAT_XC#], [P_FARVAT_XO#], and so on.

CHR: Chromosome Number

GENE: Gene name

NSAMP: The number of samples

NVARIANT: The number of variants (SNPs)

MAC: The number of allele count

P_FARVAT_XB0.5: p-value of FARVAT-XB under random XCI

P_FARVAT_XB1: p-value of FARVAT-XB under E-XCI

P_FARVAT_XB0.25: p-value of FARVAT-XB under S-XCI to normal allele

P_FARVAT_XB0.75: p-value of FARVAT-XB under S-XCI to deleterious allele

P_FARVATX_XC0.5: p-value of FARVAT-XC under random XCI

P_FARVAT_XC1: p-value of FARVAT-XC under E-XCI

P_FARVAT_XC0.25: p-value of FARVAT-XC under S-XCI to normal allele

P_FARVAT_XC0.75: p-value of FARVAT-XC under S-XCI to deleterious allele

P_FARVATX_XO0.5: p-value of FARVAT-XO under random XCI

P_FARVAT_XO1: p-value of FARVAT-XO under E-XCI

P_FARVAT_XO0.25: p-value of FARVAT-XO under S-XCI to normal allele

P_FARVAT_XO0.75: p-value of FARVAT-XO under S-XCI to deleterious allele


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