scoary - pangenome-wide association studies

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

scoary 1.6.16                                     January 2019                                         SCOARY(1)

       scoary - pangenome-wide association studies

optionalarguments:-h, --help
              show this help message and exit

   Inputoptions:-t TRAITS, --traits TRAITS
              Input trait table (comma-separated-values). Trait presence is indicated by 1, trait absence by  0.
              Assumes strain names in the first column and trait names in the first row

       -g GENES, --genes GENES
              Input  gene  presence/absence table (comma-separatedvalues) from ROARY. Strain names must be equal
              to those in the trait table

       -n NEWICKTREE, --newicktree NEWICKTREE
              Supply a custom tree (Newick format) for phylogenetic analyses instead instead of  calculating  it
              internally.

       -s START_COL, --start_col START_COL
              On  which  column  in  the gene presence/absence file do individual strain info start. Default=15.
              (1-based indexing)

       --delimiter DELIMITER
              The delimiter between cells in the gene presence/absence and trait files, as well  as  the  output
              file.

       -r RESTRICT_TO, --restrict_to RESTRICT_TO
              Use  if  you  only  want  to  analyze  a  subset  of  your  strains. Scoary will read the provided
              comma-separated table of strains and restrict analyzes to these.

   Outputoptions:-o OUTDIR, --outdir OUTDIR
              Directory to place output files. Default = .

       -u, --upgma_tree
              This flag will cause Scoary to write the calculated UPGMA tree to a newick file

       -p P_VALUE_CUTOFF [P_VALUE_CUTOFF ...], --p_value_cutoff P_VALUE_CUTOFF [P_VALUE_CUTOFF ...]
              P-value cut-off / alpha level. For Fishers, Bonferronis,  and  Benjamini-Hochbergs  tests,  SCOARY
              will  not report genes with higher p-values than this.  For empirical p-values, this is treated as
              an alpha level instead. I.e. 0.02 will filter all genes except the lower and upper percentile from
              this test. Run with "-p 1.0" to report all genes. Accepts standard form  (e.g.  1E-8).  Provide  a
              single  value  (applied  to  all)  or  exactly  as  many  values  as  correction  criteria  and in
              corresponding order. (See example under correction). Default = 0.05

       -c [{I,B,BH,PW,EPW,P} [{I,B,BH,PW,EPW,P} ...]], --correction [{I,B,BH,PW,EPW,P} [{I,B,BH,PW,EPW,P} ...]]
              Apply the indicated filtration measure. Allowed values are I, B,  BH,  PW,  EPW,  P.  I=Individual
              (naive)  p-value. B=Bonferroni adjusted p-value. BH=BenjaminiHochberg adjusted p. PW=Best (lowest)
              pairwise comparison. EPW=Entire range of pairwise comparison p-values.  P=Empirical  p-value  from
              permutations.  You  can  enter  as  many  correction  criteria  as  you  would like. These will be
              associated with the p_value_cutoffs you enter. For example "-c I EPW -p 0.1 0.05" will  apply  the
              following  cutoffs:  Naive  p-value  must  be  lower  than  0.1  AND  the entire range of pairwise
              comparison values are below 0.05 for this  gene.  Note  that  the  empirical  p-values  should  be
              interpreted  at  both  tails. Therefore, running "-c P -p 0.05" will apply an alpha of 0.05 to the
              empirical (permuted) p-values, i.e. it will filter everything  except  the  upper  and  lower  2.5
              percent of the distribution. Default = Individual p-value. (I)

       -m MAX_HITS, --max_hits MAX_HITS
              Maximum number of hits to report. SCOARY will only report the top max_hits results per trait

       --include_input_columns GRABCOLS
              Grab  columns  from  the  input Roary file. and puts them in the output. Handles comma and ranges,
              e.g.  --include_input_columns 4,6,8,16-23. The special keyword ALL will include all relevant input
              columns in the output

       -w, --write_reduced
              Use with -r if you want Scoary to create a new gene presence absence file from your reduced set of
              isolates. Note: Columns 1-14 (No. sequences, Avg group size nuc etc) in this file do  not  reflect
              the reduced dataset. These are taken from the full dataset.

       --no-time
              Output  file  in the form TRAIT.results.csv, instead of TRAIT_TIMESTAMP.csv. When used with the -w
              argument will output a reduced gene matrix in the  form  gene_presence_absence_reduced.csv  rather
              than gene_presence_absence_reduced_TIMESTAMP.csv

   Analysisoptions:-e PERMUTE, --permute PERMUTE
              Perform  N  number of permutations of the significant results post-analysis. Each permutation will
              do a label switching of the phenotype and a new  p-value  is  calculated  according  to  this  new
              dataset.  After  all N permutations are completed, the results are ordered in ascending order, and
              the percentile of the original result in the permuted p-value distribution is reported.

       --no_pairwise
              Do not perform pairwise comparisons. Inthis mode, Scoary will perform  population  structure-naive
              calculations  only.  (Fishers  test,  ORs  etc). Useful for summary operations and exploring sets.
              (Genes unique in groups, intersections etc) but not causal analyses.

       --collapse
              Add this to collapse correlated genes (genes that have  identical  distribution  patterns  in  the
              sample) into merged units.

   Miscoptions:--threads THREADS
              Number of threads to use. Default = 1

       --test Run Scoary on the test set in exampledata, overriding all other parameters.

       --citation
              Show citation information, and exit.

       --version
              Display Scoary version, and exit.

       by Ola Brynildsrud (olbb@fhi.no)

       scoary  [-h]  [-t  TRAITS]  [-g  GENES]  [-n  NEWICKTREE]  [-s  START_COL]  [--delimiter  DELIMITER]  [-r
       RESTRICT_TO]  [-o  OUTDIR]  [-u]  [-p  P_VALUE_CUTOFF  [P_VALUE_CUTOFF  ...]]    [-c   [{I,B,BH,PW,EPW,P}
       [{I,B,BH,PW,EPW,P}  ...]]] [-m MAX_HITS] [--include_input_columns GRABCOLS] [-w] [--no-time] [-e PERMUTE]
       [--no_pairwise] [--collapse] [--threads THREADS] [--test] [--citation] [--version]