.TH pacoxph 1 "4 May 2016" "ProbABEL 0.5.0"
.SH NAME
pacoxph \- Perform Genome-Wide Association Analysis using Cox' Proportional
hazards model
.SH SYNOPSIS
.B pacoxph
.RI "[ " "command-line options" " ]"
.SH DESCRIPTION
.I pacoxph
runs a linear regression on large imputed data sets in an efficient way.
.SH Options
.SS Required command line options
.TP
.BI "\-p, \-\^\-pheno" " FILE"
Read phenotype data from
.I FILE
.TP
.BI "\-i, \-\^\-info" " FILE"
Read SNP information from
.I FILE
(e.g. MLINFO file).
.TP
.BI "\-d, \-\^\-dose" " FILE"
SNP predictor (e.g. MLDOSE/MLPROB) file name.
.SS Optional command line options
.TP
.BI "\-m, \-\^\-map" " FILE"
Map file name, containing base pair positions for each SNP.
.TP
.BI "\-n, \-\^\-nids" " NUMBER"
Number of people to analyse.
.TP
.BI "\-c, \-\^\-chrom"  " FILE"
Chromosome (to be passed to output).
.TP
.BI "\-o, \-\^\-out" " FILE"
Output file name (default is
.B regression.out.txt
).
.TP
.BI "\-s, \-\^\-skipd" " NUMBER"
How many columns to skip in predictor (dose/prob) file (default is 2).
.TP
.BI "\-t, \-\^\-ntraits" " NUMBER"
How many traits are analysed (default is 2).
.TP
.BI "\-g, \-\^\-ngpreds"  " NUMBER"
How many predictor columns per marker (default 1 = MLDOSE; else use 2 for MLPROB).
.TP
.BI "\-a, \-\^\-separat" " CHAR"
Use character \fICHAR\fR to separate fields in the output file(s) (default is space).
.TP
.B \-r, \-\^\-score
Use the score test.
.TP
.B \-e, \-\^\-no-head
Do not report header line in the output.
.TP
.B \-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 \fBFreq1\fR column in the info file (see the \fI--info\fR
option) is > 0.5 and if so will flip the probabilities/dosage of that
variant such that \fBA1\fR and \fBA2\fR are interchanged. This will
add a column called \fBAllelesFlipped\fR to the output file(s),
indicating whether the alleles were flipped (1) or not (0).
.TP
.B \-l \-\^\-allcov
Report estimates for all covariates (large outputs!).
.TP
.BI "\-b, \-\^\-interaction" " NUMBER"
Which covariate to use for interaction with SNP analysis (default is no interaction, 0). \fINUMBER\fR indicates the column number of the covariate.
.TP
.B \-\^\-help
Print help.

.SH "SEE ALSO"
probabel(1), palinear(1), palogist(1)
.SH BUGS
The bugtracker is located at
.br
https://github.com/GenABEL-Project/ProbABEL/issues
.SH AUTHORS
Lennart C. Karssen