The bioBakery help forum

Decomposition method not available in recent halla versions?

Hi,

I am using Halla version 0.8.17 and noticed some inconsistencies between this version and the documentation at https://github.com/biobakery/halla#markdown-header-basic-usage

e.g. in the docs, there is the following

usage: halla [-h] [--version] -X <input_dataset_1.txt>
             [-Y <input_dataset_2.txt>] -o <output> [-q <.1>]
             [-p {ecdf,gpd,none}] [-a {HAllA,AllA}] [-i <1000>]
             [-m {nmi,ami,mic,dmic,dcor,pearson,spearman}]
             [-d {none,mca,pca,ica,cca,kpca,pls,medoid}]
             [--fdr {bh,by,bonferroni,no_adjusting}] [-v VERBOSE]
             [--diagnostics-plot] [--discretizing {equal-area,hclust,none}]
             [--linkage {single,average,complete,weighted}]
             [--apply-stop-condition] [--generate-one-null-samples] [--header]
             [--format-feature-names] [--nproc <1>] [--nbin <None>] [-s SEED]
             [-e ENTROPY_THRESHOLD] [-e1 ENTROPY_THRESHOLD1]
             [-e2 ENTROPY_THRESHOLD2] [--missing-char MISSING_CHAR]
             [--missing-method {mean,median,most_frequent}]
             [--missing-data-category] [--write-hypothesis-tree]
             [-t {log,sqrt,arcsin,arcsinh,}]

and in the version I am running, I see:

usage: halla [-h] [--version] -X <input_dataset_1.txt>
                     [-Y <input_dataset_2.txt>] -o <output> [-q <.1>] [--fnt <.25>]
                     [-p {ecdf,gpd,none}] [-a {HAllA,AllA}] [-i <1000>]
                     [-m {nmi,ami,mic,dmic,dcor,pearson,spearman,r2,chi,mi}]
                     [--fdr {bh,by,y,meinshausen,bonferroni,no_adjusting}]
                     [-v VERBOSE] [--diagnostics-plot]
                     [--discretizing {equal-freq,hclust,jenks,none}]
                     [--linkage {single,average,complete,weighted}]
                     [--generate-one-null-samples] [--header] [--format-feature-names]
                     [--nproc <1>] [--nbin <None>] [-s SEED] [-e ENTROPY_THRESHOLD]
                     [-e1 ENTROPY_THRESHOLD1] [-e2 ENTROPY_THRESHOLD2]
                     [--missing-char MISSING_CHAR]
                     [--fill-missing {mean,median,most_frequent}]
                     [--missing-data-category] [--write-hypothesis-tree]
                     [-t {log,sqrt,arcsin,arcsinh,}]

In particular, I would like to know what happened to the decomposition option? If this has been removed, what decomposition method is halla now using as standard?

Thanks,

Ramiro