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

--positive_only

only test words with a predicted positive effect direction

--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

-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.