seer1
Sequence element enrichment analysis
Overview
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:
|
dsm kmer output file |
|---|---|
|
.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:
--threadsarg (=1)-
number of threads. Suggested: 4
Filtering options:
-
--no_filtering -
turn off all filtering and peform tests on all kmers input
|
maximum kmer length |
|---|---|
|
minimum kmer frequency |
-
--min_words arg -
minimum kmer occurrences. Overrides
--maf
|
p-value threshold for initial chi squared test. Set to 1 to show all |
|---|---|
|
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
Releases
Unchanged in 5 releases since Debian 9 (Stretch).