File formats#

Details of input file formats: .ma | .besd | .epi | .esi | .query.gz | .gsam | .flist | .pheno | .plist | .eigen.gene.bin | .eigen.gene.info | .eigen.gene.snp.info | .eigen.ldblock.bin | .eigen.ldblock.info | .eigen.ldblock.snp.info

Details of output file formats: .gene.hsqRes | .gene.snpRes.gz | .log | .parRes | .snpRes

.ma#

A .ma file typically contains tab-separated columns with allele frequency and summary statistics information.

Column

Description

SNP

SNP identifier (e.g., rsID)

A1

Effect allele

A2

Non-effect allele

freq

Frequency of the effect allele (A1)

b

Effect size estimate (regression coefficient)

se

Standard error of the effect size

P

P-value for the association test

N

P-value for the association test

Example of a .ma File#

SNP      A1   A2     FRQ    b     se     P        N
rs12345   A    G    0.45   0.02   0.01   0.001    10000
rs67890   C    T    0.12  -0.03   0.02   0.05     10000

.besd#

.epi#

Individual-level gene information#

Column

Description

Chr

Chromosome number

GeneID

Gene or probe identifier (e.g., ENSG ID)

WinLength

Start position of gene

midPos

End position of gene

N

gene sample size

Orientation

Strand orientation (e.g., NA for unstranded data)

.esi#

Individual-level gene information#

Column

Description

Chrom

Chromosome number

ID

SNP identifier (e.g., rsID)

GenPos

Genetic position (in Morgans or centiMorgans)

PhysPos

Physical position on the chromosome (base pairs)

A1

Effect allele

A2

Non-effect allele

A1Freq

Frequency of the effect allele (A1)

.query.gz#

A more flexible compressed data format for molecular summary statistics#

Column

Description

GeneID

Ensembl gene ID (e.g., ENSG00000187905)

GeneChr

Chromosome number of the gene

GeneLength

Length of the gene (may be -999 if unavailable)

GenePhyPos

Physical position of the gene (in base pairs)

SNPID

SNP identifier (e.g., rs428214)

SNPChr

Chromosome number of the SNP

SNPPhyPos

Physical position of the SNP (in base pairs)

A1

Effect allele

A2

Non-effect allele

A1Freq

Frequency of the effect allele (A1)

BETA

Effect size estimate for the SNP on the gene

SE

Standard error of the effect size

Pvalue

p-value of the association

N

Sample size used in the analysis

.gsam#

Description of .gsam (two-columns format)#

Column

Description

GeneID

gene unique ID

N

per gene sample size
Description of .gsam (three-columns format)#

Column

Description

GeneID

gene unique ID

SNPID

SNP ID

N

sample size for gene-snp pair

.flist#

Individual-level gene information#

Column

Description

Chr

Chromosome number

GeneID

Gene or probe identifier (e.g., ENSG ID)

Start

Start position of gene

end

End position of gene

Orientation

Strand orientation (e.g., NA for unstranded data)

genePath

Path to the .pheno file containing molecular phenotypes

.pheno#

.plist#

Gene-Level Summary Information#

Column

Description

Chr

Chromosome number

ProbeID

Gene or probe identifier (e.g., ENSG ID)

GeneticDistance

Genetic distance (in Morgans or centiMorgans)

ProbeBp

Physical position of the probe (base pairs)

Gene

Gene symbol or identifier

N

Sample size used for analysis

Orientation

Strand orientation (e.g., NA for unstranded data)

PathOfEsd

Path to the .esd file containing simulation or effect size data

.eigen.gene.bin#

.eigen.gene.info#

.eigen.gene.snp.info#

Description of .eigen.gene.snp.info#

Column

Description

Chrom

Chromosome number

ID

SNP identifier (e.g., rsID)

GenPos

Genetic position (in Morgans or centiMorgans)

PhysPos

Physical position on the chromosome (base pairs)

A1

Effect allele

A2

Non-effect allele

A1Freq

Frequency of the effect allele (A1)

N

Sample size used for analysis

.eigen.ldblock.bin#

.eigen.ldblock.info#

Description of .eigen.ldblock.info#

Column

Description

Chrom

Chromosome number

LDBLOCK

Linkage Disequilibrium (LD) block identifier

start

Start position of the LD block (base pairs)

end

End position of the LD block (base pairs)

snpInLdBlock

Representative SNP in the LD block

NumSnpInLdBlock

Total number of SNPs within the LD block

.eigen.ldblock.snp.info#

Description of .eigen.ldblock.snp.info#

Column

Description

Chrom

Chromosome number

ID

SNP identifier (e.g., rsID)

GenPos

Genetic position (in Morgans or centiMorgans)

PhysPos

Physical position on the chromosome (base pairs)

A1

Effect allele

A2

Non-effect allele

A1Freq

Frequency of the effect allele (A1)

N

Sample size used for analysis

.gene.hsqRes#

.gene.snpRes.gz#

.log#

.parRes#

.snpRes#

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