# Decomposition method not available in recent halla versions?

**URL:** <https://forum.biobakery.org/t/decomposition-method-not-available-in-recent-halla-versions/1153>\
**Category:** HAllA\
**Created:** [October 13, 2020, 9:05am UTC](https://forum.biobakery.org/t/decomposition-method-not-available-in-recent-halla-versions/1153 "2020-10-13T09:05:14Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Ricardo\_Ramiro](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/ricardo_ramiro/32/269_2.png) [@Ricardo\_Ramiro](https://forum.biobakery.org/u/Ricardo_Ramiro)\
**Post date:** [October 13, 2020, 9:05am UTC](https://forum.biobakery.org/t/decomposition-method-not-available-in-recent-halla-versions/1153/1 "2020-10-13T09:05:14Z")

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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](https://github.com/biobakery/halla#markdown-header-basic-usage)

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

```auto
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:

```auto
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

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<div class="post-metadata">

**Author:** ![andrewGhazi](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/andrewghazi/32/2950_2.png) [@andrewGhazi](https://forum.biobakery.org/u/andrewGhazi)\
**Post date:** [December 21, 2020, 6:36pm UTC](https://forum.biobakery.org/t/decomposition-method-not-available-in-recent-halla-versions/1153/2 "2020-12-21T18:36:36Z")

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

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<div class="post-metadata">

**Author:** ![Ricardo\_Ramiro](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/ricardo_ramiro/32/269_2.png) [@Ricardo\_Ramiro](https://forum.biobakery.org/u/Ricardo_Ramiro)\
**Post date:** [December 21, 2020, 7:22pm UTC](https://forum.biobakery.org/t/decomposition-method-not-available-in-recent-halla-versions/1153/3 "2020-12-21T19:22:43Z")

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thanks for the clarification