pacoxph(1)

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.