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.

March 2017

seer 1.1.2