NAME

       scoary - pangenome-wide association studies

SYNOPSIS

       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]

OPTIONS

   optional arguments:
       -h, --help
              show this help message and exit

   Input options:
       -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.

   Output options:
       -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

   Analysis options:
       -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.

   Misc options:
       --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)

AUTHOR

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