table of contents
| KMDS(1) | User Commands | KMDS(1) |
NAME¶
kmds - control for population structure
DESCRIPTION¶
Control for population structure. Filter kmers and create a matrix representing population structure.
This program belongs to seer(1) (Sequence Element (kmer) Enrichment Analysis).
OPTIONS¶
1) filter and subsample with --no_mds and --size
2) combine, and do metric multidimensional scaling with --mds_concat
Required options:¶
- -k [ --kmers ] arg
- dsm kmer output file
- -p [ --pheno ] arg
- .pheno metadata
MDS options:¶
- -o [ --output ] arg
- output prefix for new dsm file
- --no_mds
- do not perform MDS; output subsampled matrix instead
- --write_distances
- write csv of distance matrix
- --mds_concat arg
- list of subsampled matrices to use in MDS. Performs only MDS; implies --no_filtering
- --pc arg (=3)
- number of principal coordinates to output
- --size arg (=1000000)
- number of kmers to use in MDS
- --threads arg (=1)
- number of threads. Suggested: 4
Filtering options:¶
- --no_filtering
- turn off all filtering and do not output new kmer file
- --max_length arg (=100)
- maximum kmer length
- --maf arg (=0.01)
- minimum kmer frequency
- --min_words arg
- minimum kmer occurrences. Overrides --maf
Other options:¶
- --version
- prints version and exits
- -h [ --help ]
- full help message
EXAMPLE¶
Filter kmers and create a matrix representing population structure with kmds
- kmds -k dsm_input.txt.gz --pheno metadata.pheno -o filtered
To spread this process out, run the following command on each dsm file
- kmds -k dsm_input.txt.gz --pheno metadata.pheno --no_mds --size 10000
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 | kmds 1.1.2 |