---
name: "pacoxph"
section: "1"
platform: "linux"
package: "probabel"
version: "0.5.0+dfsg-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/pacoxph"
---

# pacoxph(1)

Perform Genome-Wide Association Analysis using Cox' Proportional hazards model

## NAME

pacoxph - Perform Genome-Wide Association Analysis using Cox' Proportional hazards model

## SYNOPSIS

**pacoxph** \[ *command-line options* \]

## DESCRIPTION

*pacoxph* runs a linear regression on large imputed data sets in an efficient way.

## Options

### Required command line options

- **-p, --pheno** *FILE*

  Read phenotype data from *FILE*

- **-i, --info** *FILE*

  Read SNP information from *FILE* (e.g. MLINFO file).

- **-d, --dose** *FILE*

  SNP predictor (e.g. MLDOSE/MLPROB) file name.

### Optional command line options

- **-m, --map** *FILE*

  Map file name, containing base pair positions for each SNP.

- **-n, --nids** *NUMBER*

  Number of people to analyse.

- **-c, --chrom** *FILE*

  Chromosome (to be passed to output).

- **-o, --out** *FILE*

  Output file name (default is **regression.out.txt** ).

- **-s, --skipd** *NUMBER*

  How many columns to skip in predictor (dose/prob) file (default is 2).

- **-t, --ntraits** *NUMBER*

  How many traits are analysed (default is 2).

- **-g, --ngpreds** *NUMBER*

  How many predictor columns per marker (default 1 = MLDOSE; else use 2 for MLPROB).

- **-a, --separat** *CHAR*

  Use character *CHAR* to separate fields in the output file(s) (default is space).

- **-r, --score**

  Use the score test.

- **-e, --no-head**

  Do not report header line in the output.

- **-f --flipmaf**

  Flip reference and effect allele according to Minor Allele Frequency (MAF) such that the minor allele is the effect/predictor allele. If this option is set, ProbABEL will check for each genetic variant whether the **Freq1** column in the info file (see the *--info* option) is \> 0.5 and if so will flip the probabilities/dosage of that variant such that **A1** and **A2** are interchanged. This will add a column called **AllelesFlipped** to the output file(s), indicating whether the alleles were flipped (1) or not (0).

- **-l --allcov**

  Report estimates for all covariates (large outputs!).

- **-b, --interaction** *NUMBER*

  Which covariate to use for interaction with SNP analysis (default is no interaction, 0). *NUMBER* indicates the column number of the covariate.

- **--help**

  Print help.

## SEE ALSO

[probabel(1)](/probabel/1.md), [palinear(1)](/palinear/1.md), [palogist(1)](/palogist/1.md)

## BUGS

The bugtracker is located at\
 https://github.com/GenABEL-Project/ProbABEL/issues

## AUTHORS

Lennart C. Karssen