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Deprecating groupCol and blockCol #62

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Deprecating groupCol and blockCol #62

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36b2cd1
changed all mentions of group in folder R/;example: lgroupf etc to cl…
asyakhl Sep 14, 2024
2e42c3e
changed all mentions of group in folder inst/scripts/ to class and sa…
asyakhl Sep 14, 2024
2078503
changed all mentions of group in folder tests/ to class and same was …
asyakhl Sep 14, 2024
dd3681c
changed all mentions of group in folder vignettes/ to class and same …
asyakhl Sep 14, 2024
be5d289
changed all mentions of group in DESCRIPTION file to class
asyakhl Sep 14, 2024
75e86a0
three man files updated with class to replace group and subclass to r…
asyakhl Sep 14, 2024
55ea930
formally deprecating groupCol and blockCol arguments
asyakhl Sep 17, 2024
e92e660
updating attributes to match updated arguments
asyakhl Sep 17, 2024
6f155b6
fixing typo
asyakhl Sep 17, 2024
bfa65a7
adding warnings for deprecated args groupCol and blockCol
asyakhl Sep 21, 2024
22a2a2d
updating attributes to match updated arguments
asyakhl Sep 21, 2024
16bff41
resolve merge conflict for DESCRIPTION
asyakhl Sep 22, 2024
60234f9
resolve merge conflict for DESCRIPTION
asyakhl Sep 22, 2024
40a8ee2
renaming groups to classes
asyakhl Sep 22, 2024
0e3a84d
resolving merge conflict for lefserPlotFeat.R
asyakhl Sep 22, 2024
90c9d2d
resolving merge conflict for inst/scripts/histogramPlot.R
asyakhl Sep 22, 2024
02e5027
merged devel into deprecation and resolved all merge conflicts
asyakhl Sep 22, 2024
483edeb
renaming refGrp to refClass
asyakhl Sep 22, 2024
f9c07d5
renaming group and block to class and subclass for tests/testthat/tes…
asyakhl Sep 22, 2024
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8 changes: 5 additions & 3 deletions R/lefser.R
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@asyakhl You should .Deprecated the old arguments as expr.

Original file line number Diff line number Diff line change
Expand Up @@ -231,7 +231,9 @@ lefser <-
checkAbundances = TRUE,
method = "none",
...,
expr
expr,
groupCol = "GROUP",
blockCol = NULL
) {
if (!missing(expr)) {
.Deprecated(
Expand Down Expand Up @@ -325,8 +327,8 @@ lefser <-
attr(res_scores, "kth") <- kruskal.threshold
attr(res_scores, "wth") <- wilcox.threshold
attr(res_scores, "ldath") <- lda.threshold
attr(res_scores, "grp") <- classCol
attr(res_scores, "blk") <- subclassCol
attr(res_scores, "class") <- classCol
attr(res_scores, "subclass") <- subclassCol
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@asyakhl Were these updated in lefsePlotFeat.R ?

attr(res_scores, "method") <- method
attr(res_scores, "lclassf") <- lclassf[1]
res_scores
Expand Down
15 changes: 7 additions & 8 deletions vignettes/lefser.Rmd
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Expand Up @@ -31,14 +31,13 @@ The original software utilizes standard statistical significance tests along
with supplementary tests that incorporate biological consistency and the
relevance of effects to identity the features (e.g., organisms, clades, OTU,
genes, or functions) that are most likely to account for differences between
the two sample classes of interest, referred as ‘classes’. While *LEfSe* is
widely used and available in different platform such as Galaxy UI and Conda,
there is no convenient way to incorporate it in R-based workflows. Thus, we
re-implement *LEfSe* as an R/Bioconductor package, *lefser*. Following the
*LEfSe*‘s algorithm including Kruskal-Wallis test, Wilcoxon-Rank Sum test,
and Linear Discriminant Analysis, with some modifications, *lefser*
successfully reproduces and improves the original statistical method and
the associated plotting functionality.
the two sample classes of interest. While *LEfSe* is widely used and available
in different platform such as Galaxy UI and Conda, there is no convenient way
to incorporate it in R-based workflows. Thus, we re-implement *LEfSe* as
an R/Bioconductor package, *lefser*. Following the *LEfSe*‘s algorithm including
Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis,
with some modifications, *lefser* successfully reproduces and improves the
original statistical method and the associated plotting functionality.

[LEfSe]: https://huttenhower.sph.harvard.edu/galaxy/
[Huttenhower et al. 2011]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218848/
Expand Down