kmds1
Control for population structure
Overview
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:
|
dsm kmer output file |
|---|---|
|
.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
|
number of principal coordinates to output |
|---|---|
|
number of kmers to use in MDS |
|
number of threads. Suggested: 4 |
Filtering options:
-
--no_filtering -
turn off all filtering and do not output new kmer file
|
maximum kmer length |
|---|---|
|
minimum kmer frequency |
-
--min_words arg -
minimum kmer occurrences. Overrides
--maf
Other options:
-
--version -
prints version and exits
-
-h [ --help ] -
full help message
Examples
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
Releases
Unchanged in 5 releases since Debian 9 (Stretch).