pacoxph - Perform Genome-Wide Association Analysis using Cox' Proportional hazards model

       Lennart C. Karssen

ProbABEL 0.5.0                                     4 May 2016                                         pacoxph(1)

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

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

       pacoxph - Perform Genome-Wide Association Analysis using Cox' Proportional hazards model

Requiredcommandlineoptions-p,--phenoFILE
              Read phenotype data from FILE-i,--infoFILE
              Read SNP information from FILE (e.g. MLINFO file).

       -d,--doseFILE
              SNP predictor (e.g. MLDOSE/MLPROB) file name.

   Optionalcommandlineoptions-m,--mapFILE
              Map file name, containing base pair positions for each SNP.

       -n,--nidsNUMBER
              Number of people to analyse.

       -c,--chromFILE
              Chromosome (to be passed to output).

       -o,--outFILE
              Output file name (default is regression.out.txt ).

       -s,--skipdNUMBER
              How many columns to skip in predictor (dose/prob) file (default is 2).

       -t,--ntraitsNUMBER
              How many traits are analysed (default is 2).

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

       -a,--separatCHAR
              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,--interactionNUMBER
              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.

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

pacoxph [ command-lineoptions ]