palogist [ command-line options ]


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


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 1).

-g, -\^-ngpreds NUMBER

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

-a, -\^-separat FILE

Character to separate fields (default is space).

-r, -\^-score

Use the score test.

-e, -\^-no-head

Do not report header line in the output.

-l -\^-allcov

Report estimates for all covariates (large outputs!).

-b, -\^-interaction

Which covariate to use for interaction with SNP analysis (default is no interaction, 0).

-k, -\^-interaction_only

Like -\^-interaction but without covariate acting in interaction with SNP (default is no interaction, 0).

-v, -\^-mmscore FILE

Score test in samples of related individuals. The FILE argument is the name of a file with the inverse correlation matrix. NOTE THAT THIS FEATURE IS STILL EXPERIMENTAL!


Report robust (a.k.a. sandwich, a.k.a. Hubert-White) standard errors.


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Lennart C. Karssen