Mercurial > repos > eschen42 > w4mcorcov
diff w4mcorcov.xml @ 12:ddaf84e15d06 draft
planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
| author | eschen42 |
|---|---|
| date | Thu, 08 Nov 2018 23:06:09 -0500 |
| parents | ddcc33ff3205 |
| children | 2ae2d26e3270 |
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--- a/w4mcorcov.xml Wed Sep 05 22:31:21 2018 -0400 +++ b/w4mcorcov.xml Thu Nov 08 23:06:09 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.15"> +<tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.16"> <description>OPLS-DA Contrasts of Univariate Results</description> <macros> <xml name="paramPairSigFeatOnly"> @@ -201,13 +201,13 @@ <has_text text="level1Level2Sig" /> <!-- first matched line --> <has_text text="M349.2383T700" /> - <has_text text="-0.3704185" /> + <has_text text="-0.462909875" /> <has_text text="-36.6668927" /> <has_text text="0.4914638" /> <has_text text="0.01302117" /> <!-- second matched line --> <has_text text="M207.9308T206" /> - <has_text text="0.3235022" /> + <has_text text="0.504885262" /> <has_text text="5.97529097" /> <has_text text="0.207196379" /> <has_text text="0.04438632" /> @@ -259,7 +259,7 @@ <has_text text="level1Level2Sig" /> <!-- first matched line --> <has_text text="M200.005T296" /> - <has_text text="-0.24533821" /> + <has_text text="-0.28035717" /> <has_text text="-3.3573953" /> <has_text text="0.1157346" /> <has_text text="0.0647860" /> @@ -309,13 +309,13 @@ <has_text text="vip4o" /> <!-- first matched line --> <has_text text="M349.2383T700" /> - <has_text text="-0.37867079" /> + <has_text text="-0.4732226665" /> <has_text text="-37.71066" /> <has_text text="0.5246766" /> <has_text text="0.0103341" /> <!-- second matched line --> <has_text text="M207.9308T206" /> - <has_text text="0.31570433" /> + <has_text text="0.4927151212" /> <has_text text="5.86655640" /> <has_text text="0.2111623" /> <has_text text="0.0488654" /> @@ -368,7 +368,7 @@ <has_text text="NM516T251" /> <has_text text="flower_yes" /> <has_text text="other" /> - <has_text text="0.03402807" /> + <has_text text="0.3499550705" /> <has_text text="0.03526926" /> <has_text text="0.43664386" /> <has_text text="0.587701897" /> @@ -419,13 +419,13 @@ <has_text text="vip4o" /> <!-- first matched line --> <has_text text="M349.2383T700" /> - <has_text text="0.43361563" /> + <has_text text="0.61594030" /> <has_text text="37.76875778" /> <has_text text="0.54672558" /> <has_text text="0.3920409" /> <!-- second matched line --> <has_text text="M207.9308T206" /> - <has_text text="-0.3365475" /> + <has_text text="-0.89716403" /> <has_text text="-6.337903" /> <has_text text="0.270297" /> <has_text text="0.037661" /> @@ -454,14 +454,14 @@ <has_text text="vip4o" /> <!-- first matched line --> <has_text text="M349.2383T700" /> - <has_text text="-0.0435663" /> - <has_text text="-1.9068114" /> - <has_text text="0.0304592" /> - <has_text text="0.104748883" /> + <has_text text="-0.331230562" /> + <has_text text="-2.47167915" /> + <has_text text="0.0892595" /> + <has_text text="0.0049228872" /> </assert_contents> </output> </test> - <!-- test #6 - issue 8 --> + <!-- test #7 - issue 8 --> <test> <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> <param name="sampleMetadata_in" value="issue8_input_sampleMetadata.tsv"/> @@ -495,6 +495,7 @@ **Author** - Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu) +**Release Notes** - https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper#release-notes Motivation ---------- @@ -616,9 +617,13 @@ | [OUT] Contrast-detail output PDF - | Several plots for each two-projection OPLS-DA analysis: + | File containing several plots for each two-projection OPLS-DA analysis. + +- (first row, left) **correlation-versus-covariance plot** of OPLS-DA results -- (first row, left) **correlation-versus-covariance plot** of OPLS-DA results (a work-alike for the S-PLOT, computed using formula in Supplement to Wiklund, *op. cit.*); point-color becomes saturated as the "variable importance in projection to the predictive components" (VIP\ :subscript:`4,p` from Galindo-Prieto *et al.* 2014) ranges from 0.83 and 1.21 (Mehmood *et al.* 2012), for use to identify features for consideration as biomarkers. + - This is a work-alike for the S-PLOT, computed using formula in equations 1 and 2 from Wiklund, (*op. cit.*); + - point-color becomes saturated as the "variable importance in projection to the predictive components" (VIP\ :subscript:`4,p` from Galindo-Prieto *et al.* 2014) increases through the range from 0.83 and 1.21 (Mehmood *et al.* 2012), for use to identify features for consideration as biomarkers; + - plot symbols are diamonds when the adjusted p-value of correlation is greater than 0.05, circles when it is less than 0.01, and triangles when it between these limits. - (second row, left) **model-overview plot** for the two projections; grey bars are the correlation coefficient for the fitted data; black bars indicate performance in cross-validation tests (Th]]>é<![CDATA[venot, 2017) - (first row, right) OPLS-DA **scores-plot** for the two projections (Th]]>é<![CDATA[venot *et al.*, 2015) - (second row, right) **correlation-versus-covariance plot** of OPLS-DA results **orthogonal to the predictor** (see section "S-Plot of Orthogonal Component" in Wiklund, *op. cit.*, pp. 120-121; this characterizes features with the greatest variation independent of the predictor). @@ -633,12 +638,18 @@ - **featureID** - feature-identifier - **factorLevel1** - factor-level 1 - **factorLevel2** - factor-level 2 (or "other" when contrasting factor-level 1 with all other levels) -- **correlation** - correlation of the features projection explaining the difference between the features, < 0 when intensity for level 1 is greater (from formula in Supplement to Wiklund, *op. cit.*). Note that, for a given contrast, there is a linear relationship between 'loadp' and 'correlation'. -- **covariance** - covariance of the features projection explaining the difference between the features, < 0 when intensity for level 1 is greater (from formula in *ibid.*) +- **correlation** - correlation of the features projection explaining the difference between the features, < 0 when intensity for level 1 is greater (from equation 2 in Wiklund, *op. cit.*). Note that, for a given contrast, there is a linear relationship between 'loadp' and 'correlation'. +- **covariance** - relative covariance of the features projection explaining the difference between the features, < 0 when intensity for level 1 is greater (from formula in *ibid.*, but scaled so that the greatest value has a magnitude of 1) - **vip4p** - "variable importance in projection" to the predictive projection, VIP\ :subscript:`4,p` (Galindo-Prieto *op. cit.*) - **vip4o** - "variable importance in projection" to the orthogonal projection, VIP\ :subscript:`4,o` (*ibid.*) - **loadp** - variable loading for the predictive projection (Wiklund *op. cit.*) - **loado** - variable loading for the orthogonal projection (*ibid.*) +- **cor_p_val_raw** - p-value for Fisher-transformed correlation (Fisher, 1921; Snedecor, 1980; see also https://en.wikipedia.org/wiki/Fisher_transformation), with no family-wise error-rate correction. +- **cor_p_value** - p-value for Fisher-transformed correlation, adjusted for family-wise error rate (Yekutieli *et al.*, 2001). Caveat: any previous selection for features that vary notably by factor level may result in too little adjustment. +- **cor_ci_lower** - lower limit of 95% confidence interval for correlation (see e.g. https://en.wikipedia.org/wiki/Fisher_transformation) +- **cor_ci_upper** - upper limit of 95% confidence interval for correlation (*ibid.*) +- **mz** - *m/z* ratio for feature, copied from input variableMetadata +- **rt** - retention time for feature, copied from input variableMetadata - **level1Level2Sig** - (Only present when a test other than "none" is chosen) '1' when feature varies significantly across all classes (i.e., not pair-wise); '0' otherwise [OUT] Feature "Salience" data TABULAR @@ -819,6 +830,19 @@ <citations> <!-- this tool --> <citation type="doi">10.5281/zenodo.1034784</citation> + <!-- Fisher_1921: Fisher z-transformation of correlation coefficient --> + <citation type="bibtex"><![CDATA[ + @article{Fisher_1921, + author = {Fisher, R. A.}, + title = {{On the probable error of a coefficient of correlation deduced from a small sample}}, + journal = {Metron}, + year = {1921}, + volume = {1}, + pages = {3--32}, + note = {Defines the Fisher z-transformation of a coefficient of correlation. Citation adapted from http://www.citeulike.org/group/894/article/2344770}, + url = {https://digital.library.adelaide.edu.au/dspace/bitstream/2440/15169/1/14.pdf}, + } + ]]></citation> <!-- Galindo_Prieto_2014 Variable influence on projection (VIP) for OPLS --> <citation type="doi">10.1002/cem.2627</citation> <!-- Giacomoni_2014 W4M 2.5 --> @@ -833,6 +857,22 @@ <citation type="doi">10.3389/fmolb.2016.00026</citation> <!-- Sun_2016 Urinary Biomarkers for adolescent idiopathic scoliosis --> <citation type="doi">10.1038/srep22274</citation> + <!-- Snedecor_1980: Fisher z-transformation of correlation coefficient --> + <citation type="bibtex"><![CDATA[ + @book{Snedecor_1980, + author = {Snedecor, George W. and Cochran, William G.}, + title = {Statistical methods}, + publisher = {Iowa State University Press}, + year = {1980}, + pages = {186}, + isbn = {0813815606}, + language = {eng}, + keyword = {Statistics, Statistics as Topic -- methods}, + lccn = {80014582}, + edition = {7th ed..}, + address = {Ames, Iowa}, + } + ]]></citation> <!-- Thevenot_2015 Urinary metabolome statistics --> <citation type="doi">10.1021/acs.jproteome.5b00354</citation> <!-- ropls package --> @@ -849,6 +889,8 @@ ]]></citation> <!-- Wiklund_2008 OPLS PLS-DA and S-PLOT --> <citation type="doi">10.1021/ac0713510</citation> + <!-- Yekutieli_2001 The control of the false discovery rate in multiple testing under dependency --> + <citation type="doi">10.1214/aos/1013699998</citation> </citations> <!-- vim:et:sw=4:ts=4