pacoxph1
Perform genome-wide association analysis using cox' proportional hazards model
Usage
pacoxph [command-line
options]
Overview
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
Freq1column in the info file (see the --info option) is > 0.5 and if so will flip the probabilities/dosage of that variant such thatA1andA2are interchanged. This will add a column calledAllelesFlippedto 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.
Releases
6 releases since Debian 8 (Jessie); the text changed 2 times.
--flipmaf since Debian 10 (Buster);
-f since Debian 10 (Buster).
--interaction until Debian 9 (Stretch);
--interaction_only until Debian 9 (Stretch);
--separat until Debian 9 (Stretch);
-a until Debian 9 (Stretch);
-b until Debian 9 (Stretch);
-k until Debian 9 (Stretch).