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pacoxph(1) General Commands Manual pacoxph(1)

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

Read phenotype data from FILE
Read SNP information from FILE (e.g. MLINFO file).
SNP predictor (e.g. MLDOSE/MLPROB) file name.

Optional command line options

Map file name, containing base pair positions for each SNP.
Number of people to analyse.
Chromosome (to be passed to output).
Output file name (default is regression.out.txt ).
How many columns to skip in predictor (dose/prob) file (default is 2).
How many traits are analysed (default is 2).
How many predictor columns per marker (default 1 = MLDOSE; else use 2 for MLPROB).
Use character CHAR to separate fields in the output file(s) (default is space).
Use the score test.
Do not report header line in the output.
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).
Report estimates for all covariates (large outputs!).
Which covariate to use for interaction with SNP analysis (default is no interaction, 0). NUMBER indicates the column number of the covariate.
Print help.

SEE ALSO

probabel(1), palinear(1), palogist(1)

BUGS

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

AUTHORS

Lennart C. Karssen

4 May 2016 ProbABEL 0.5.0