Instructions


FARVATX as of January 11, 2018

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


Instructions


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: 

그림1

1.1.2 MAP FILE

Each line of the MAP file describes a single marker and must contain 4 columns:

그림2

1.2. Phenotype data

Sample lines of phenotype and covariates file. (tab or space delimited)

그림3

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.

그림4

 

2. Create Kinship Coefficient Matrix 

그림8

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

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