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

Hi Ramiro, HAllA no longer provides any dimension reduction functionality, so that option has been removed.

thanks for the clarification