NAME

       seer - sequence element enrichment analysis

DESCRIPTION

       Sequence Element Enrichment Analysis

       The .pheno file format is tab separated, two columns with sample name, one with phenotype.
       Phenotypes of only 0 or 1 will be treated as binary, any other  value  and  the  phenotype
       will  be treated as quantitative. Therefore for missing phenotype values the sample should
       simply be excluded from this file.

OPTIONS

   Required options:
       -k [ --kmers ] arg
              dsm kmer output file

       -p [ --pheno ] arg
              .pheno metadata

   Covariate options:
       --struct arg
              mds values from kmds

       --covar_file arg
              file containing covariates

       --covar_list arg
              list of columns covariates to use. Format is 1,2q,3 (use q for quantitative)

   Performance options:
       --threads arg (=1)
              number of threads. Suggested: 4

   Filtering options:
       --no_filtering
              turn off all filtering and peform tests on all kmers input

       --max_length arg (=100)
              maximum kmer length

       --maf arg (=0.01)
              minimum kmer frequency

       --min_words arg
              minimum kmer occurrences. Overrides --maf

       --chisq arg (=10e-5)
              p-value threshold for initial chi squared test. Set to 1 to show all

       --pval arg (=10e-8)
              p-value threshold for final logistic test. Set to 1 to show all

   Other options:
       --print_samples
              print lists of samples significant kmers were found in

       --version
              prints version and exits

       -h [ --help ]
              full help message

EXAMPLES

       Basic usage:

              seer -k dsm_input.txt.gz --pheno metadata.pheno > significant_kmers.txt

       To use the kmds output, increase execution speed and give the most complete output

              seer -k  filtered.gz  --pheno  metadata.pheno  --struct  filtered.dsm  --threads  4
              --print_samples

AUTHOR

       This  manpage was written by Andreas Tille for the Debian distribution and can be used for
       any other usage of the program.