---
name: "emmax"
section: "1"
platform: "linux"
package: "emmax"
version: "0~beta.20100307-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/emmax"
---

# emmax(1)

emmax

## NAME

emmax: - emmax

## SYNOPSIS

**emmax** \[*options*\]

## DESCRIPTION

Required parameters

**-t** \[tpedf\_prefix\] : prefix for tped/tfam files

- **-o** \[out\_prefix\]

  : output file name prefix

Likely essential parameters

**-p** \[phenof\] : 3-column phenotype file with FAMID, INDID at the first two colmns, in the same order of .tfam file. Not required only with **-K** option      **-k** \[kinf\] : n \* n matrix containing kinship values in the individual order consistent to \[tpedf\].tfam file. \[tpedf\].kinf will be used if not specified

**-c** \[covf\] : multi-column covariate file with FAMID, INDID at the first two colmns, in the same order of .tfam fileOptional parameters

**-i** \[in\_prefix\] : input file name prefix including eigenvectors

- **-d** \[# digits\]

  : precision of the output values (default : 5)

**-s** \[start index of SNP\] : start index of SNP (default : 0)

**-e** \[end index of SNP\] : end index of SNP (default : #snps)

**-w** : flag for writing eigenvalues/eigenvector files

**-D** \[delimiters\] : delimter string in quotation marks

**-P** \[# heaer cols in tped\] : # of column headers in tped file

**-F** \[# heaer cols in tfam\] : # of column headers in tfam file

Error : Unknown option character ?Usage: emmax \[options\] Required parameters

**-t** \[tpedf\_prefix\] : prefix for tped/tfam files

- **-o** \[out\_prefix\]

  : output file name prefix

Likely essential parameters

**-p** \[phenof\] : 3-column phenotype file with FAMID, INDID at the first two colmns, in the same order of .tfam file. Not required only with **-K** option      **-k** \[kinf\] : n \* n matrix containing kinship values in the individual order consistent to \[tpedf\].tfam file. \[tpedf\].kinf will be used if not specified

**-c** \[covf\] : multi-column covariate file with FAMID, INDID at the first two colmns, in the same order of .tfam fileOptional parameters

**-i** \[in\_prefix\] : input file name prefix including eigenvectors

- **-d** \[# digits\]

  : precision of the output values (default : 5)

**-s** \[start index of SNP\] : start index of SNP (default : 0)

**-e** \[end index of SNP\] : end index of SNP (default : #snps)

**-w** : flag for writing eigenvalues/eigenvector files

**-D** \[delimiters\] : delimter string in quotation marks

**-P** \[# heaer cols in tped\] : # of column headers in tped file

**-F** \[# heaer cols in tfam\] : # of column headers in tfam file