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planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
author iuc
date Wed, 26 Jun 2024 09:39:59 +0000
parents 377c2e0140b7
children
comparison
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0:377c2e0140b7 1:ea0616fb5c2d
2 <description>Microbiome Multivariable Association with Linear Models</description> 2 <description>Microbiome Multivariable Association with Linear Models</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="edam_ontology"/> 6 <expand macro="edam_ontology"/>
7 <expand macro="xrefs"/>
7 <expand macro="requirements"/> 8 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10
11 ## get column names of fixed and random effect from the input file, since galaxy
12 ## can only return indices with type="data_column"
13 ## using awk so that the file is only parsed on command line execution
14
15 #if $fixed_effects
16 #set idx = []
17 #for $i in $fixed_effects:
18 #silent idx.append(f'${i}')
19 #end for
20 #set idx_for_awk = ','.join(idx)
21
22 fixed_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk}' '$input_metadata'` &&
23 echo 'Assigned fixed effects as:' \$fixed_effects &&
24 #end if
25
26
27 #if $random_effects
28 #set idx = []
29 #for $i in $random_effects:
30 #silent idx.append(f'${i}')
31 #end for
32 #set idx_for_awk = ','.join(idx)
33
34 random_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk}' '$input_metadata'` &&
35 echo 'Assigned random effects as:' \$random_effects &&
36 #end if
37
9 ln -s '$input_data' 'input_data.tsv' 38 ln -s '$input_data' 'input_data.tsv'
10 && 39 &&
11 ln -s '$input_metadata' 'input_metadata.tsv' 40 ln -s '$input_metadata' 'input_metadata.tsv'
12 && 41 &&
13 Maaslin2.R 42 Maaslin2.R
28 #end if 57 #end if
29 #if $additional_options.analysis_method 58 #if $additional_options.analysis_method
30 --analysis_method '$additional_options.analysis_method' 59 --analysis_method '$additional_options.analysis_method'
31 #end if 60 #end if
32 #if $random_effects 61 #if $random_effects
33 --random_effects '$random_effects' 62 --random_effects \$random_effects
34 #end if 63 #end if
35 #if $fixed_effects 64 #if $fixed_effects
36 --fixed_effects '$fixed_effects' 65 --fixed_effects \$fixed_effects
37 #end if 66 #end if
67 #if $reference
68 --reference '$reference'
69 #end if
70
38 #if $additional_options.correction 71 #if $additional_options.correction
39 --correction '$additional_options.correction' 72 --correction '$additional_options.correction'
40 #end if 73 #end if
41 $additional_options.standardize 74 $additional_options.standardize
42 $output.plot_heatmap 75 $output.plot_heatmap
43 #if $output.heatmap_first_n 76 #if $output.heatmap_first_n
44 --heatmap_first_n '$output.heatmap_first_n' 77 --heatmap_first_n '$output.heatmap_first_n'
45 #end if 78 #end if
46 $output.plot_scatter 79 $output.plot_scatter
47 --cores \${GALAXY_SLOTS:-4} 80 --cores 1
48 'input_data.tsv' 81 'input_data.tsv'
49 'input_metadata.tsv' 82 'input_metadata.tsv'
50 'outputFolder' 83 'outputFolder'
51 && 84 &&
52 cd outputFolder && mkdir -p figures/ && cp *.pdf figures 85 zip -r out.zip outputFolder &&
86 cd outputFolder &&
87 mkdir -p figures/ &&
88 cp *.pdf figures
89
90
53 ]]></command> 91 ]]></command>
54 <inputs> 92 <inputs>
55 <param name="input_data" type="data" format="tabular" label="Data (or features) file"/> 93 <param name="input_data" type="data" format="tabular" label="Data (or features) file"/>
56 <param name="input_metadata" type="data" format="tabular" label="Metadata file"/> 94 <param name="input_metadata" type="data" format="tabular" label="Metadata file"/>
57 <param argument="--fixed_effects" type="select" multiple="true" optional="true" label="Interactions: Fixed effects" help="The fixed effects for the model, comma-delimited for multiple effects"> 95 <param argument="--fixed_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Interactions: Fixed effects" help="The fixed effects for the model, comma-delimited for multiple effects, Default value: All " />
58 <option value="diagnosis" selected="true">diagnosis</option> 96 <param argument="--random_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Random effects" help="The random effects for the model, comma-delimited for multiple effects, Default: None" />
59 <option value="dysbiosisnonIBD" selected="true">dysbiosisnonIBD</option> 97 <param argument="--reference" type="text" label="Reference" help="Reference for a variable with more than two levels provided as a string of 'variable,reference' comma delimited for multiple variables. " />
60 <option value="dysbiosisUC" selected="true">dysbiosisUC</option>
61 <option value="dysbiosisCD" selected="true">dysbiosisCD</option>
62 <option value="antibiotics" selected="true">antibiotics</option>
63 <option value="age" selected="true">age</option>
64 </param>
65 <param argument="--random_effects" type="text" multiple="true" optional="true" label="Random effects" help="The random effects for the model, comma-delimited for multiple effects"/>
66 <section name="additional_options" title="Additional Options" expanded="true"> 98 <section name="additional_options" title="Additional Options" expanded="true">
67 <param argument="--min_abundance" type="float" value="0.0" optional="true" label="Minimum abundance" help="The minimum abundance for each feature"/> 99 <param argument="--min_abundance" type="float" value="0.0" optional="true" label="Minimum abundance" help="The minimum abundance for each feature"/>
68 <param argument="--min_prevalence" type="float" value="0.1" optional="true" label="Minimum prevalence" help="The minimum percent of samples for which a feature is detected at minimum abundance"/> 100 <param argument="--min_prevalence" type="float" value="0.1" optional="true" label="Minimum prevalence" help="The minimum percent of samples for which a feature is detected at minimum abundance"/>
69 <param argument="--max_significance" type="float" value="0.25" optional="true" label="Maximum significance" help="The q-value threshold for significance"/> 101 <param argument="--max_significance" type="float" value="0.25" optional="true" label="Maximum significance" help="The q-value threshold for significance"/>
70 <param argument="--normalization" type="select" optional="true" label="The normalization method to apply"> 102 <param argument="--normalization" type="select" optional="true" label="The normalization method to apply">
84 <option value="LM" selected="true">LM</option> 116 <option value="LM" selected="true">LM</option>
85 <option value="CPLM">CPLM</option> 117 <option value="CPLM">CPLM</option>
86 <option value="NEGBIN">NEGBIN</option> 118 <option value="NEGBIN">NEGBIN</option>
87 <option value="ZINB">ZINB</option> 119 <option value="ZINB">ZINB</option>
88 </param> 120 </param>
89 <param argument="--correction" type="text" value="BH" optional="true" label="Correction" help="The correction method for computing the q-value"/> 121 <param argument="--correction" type="select" value="BH" optional="true" label="Correction" help="The correction method for computing the q-value, Default: BH ">
122 <option value="BH">Benjamini-Hochberg(BH)</option>
123 <option value="BY">Benjamini-Yekutieli(BY)</option>
124 <option value="Bonferroni">Bonferroni</option>
125 <option value="Holm">Holm</option>
126 <option value="Hochberg">Hochberg</option>
127 <option value="Hommel">Hommel</option>
128 </param>
90 <param argument="--standardize" type="boolean" truevalue="--standardize TRUE" falsevalue="--standardize FALSE" checked="true" label="Apply z-score so continuous metadata are on the same scale"/> 129 <param argument="--standardize" type="boolean" truevalue="--standardize TRUE" falsevalue="--standardize FALSE" checked="true" label="Apply z-score so continuous metadata are on the same scale"/>
91 </section> 130 </section>
92 <section name="output" title="Set Plotting Output" expanded="true"> 131 <section name="output" title="Set Plotting Output" expanded="true">
93 <param argument="--plot_heatmap" type="boolean" truevalue="--plot_heatmap TRUE" falsevalue="--plot_heatmap FALSE" checked="true" label="Generate a heatmap for the significant associations"/> 132 <param argument="--plot_heatmap" type="boolean" truevalue="--plot_heatmap TRUE" falsevalue="--plot_heatmap FALSE" checked="true" label="Generate a heatmap for the significant associations"/>
94 <param argument="--heatmap_first_n" type="integer" value="50" optional="true" label="Heatmap plot first N" help="In heatmap, plot top N features with significant associations"/> 133 <param argument="--heatmap_first_n" type="integer" value="50" optional="true" label="Heatmap plot first N" help="In heatmap, plot top N features with significant associations"/>
95 <param argument="--plot_scatter" type="boolean" truevalue="--plot_scatter TRUE" falsevalue="--plot_scatter FALSE" checked="true" label="Generate scatter plots for the significant associations"/> 134 <param argument="--plot_scatter" type="boolean" truevalue="--plot_scatter TRUE" falsevalue="--plot_scatter FALSE" checked="true" label="Generate scatter plots for the significant associations"/>
96 <param name="residuals_output" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Output data frame with residuals for each feature"/> 135 <param name="residuals_output" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Output data frame with residuals for each feature"/>
97 </section> 136 </section>
98 </inputs> 137 </inputs>
99 <outputs> 138 <outputs>
139 <data name="archive_output" format="zip" from_work_dir="out.zip" label="${tool.name} on ${on_string}: zip of the complete output" />
100 <data name="all_results" format="tabular" from_work_dir="outputFolder/all_results.tsv" label="All results ordered by increasing q-value"/> 140 <data name="all_results" format="tabular" from_work_dir="outputFolder/all_results.tsv" label="All results ordered by increasing q-value"/>
101 <data name="significant_results" format="tabular" from_work_dir="outputFolder/significant_results.tsv" label="Q-values smaller than or equal to the threshold"/> 141 <data name="significant_results" format="tabular" from_work_dir="outputFolder/significant_results.tsv" label="Q-values smaller than or equal to the threshold"/>
102 <data name="residuals" format="rdata" from_work_dir="outputFolder/residuals.rds" label="Data frame with residuals for each feature"> 142 <data name="residuals" format="rdata" from_work_dir="outputFolder/fits/residuals.rds" label="Data frame with residuals for each feature">
103 <filter>output['residuals_output'] is True</filter> 143 <filter>output['residuals_output'] is True</filter>
104 </data> 144 </data>
105 <data format="pdf" name="headmap" from_work_dir="outputFolder/figures/heatmap.pdf" label="Heatmap of the significant associations" > 145 <data format="pdf" name="headmap" from_work_dir="outputFolder/figures/heatmap.pdf" label="Heatmap of the significant associations" >
106 <filter>output['plot_heatmap'] is True</filter> 146 <filter>output['plot_heatmap'] is True</filter>
107 </data> 147 </data>
109 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="outputFolder/figures/" format="pdf"/> 149 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="outputFolder/figures/" format="pdf"/>
110 <filter>output['plot_scatter'] is True</filter> 150 <filter>output['plot_scatter'] is True</filter>
111 </collection> 151 </collection>
112 </outputs> 152 </outputs>
113 <tests> 153 <tests>
114 <test expect_num_outputs="5"> 154 <test expect_num_outputs="6">
115 <param name="input_data" value="HMP2_taxonomy.tsv"/> 155 <param name="input_data" value="HMP2_taxonomy.tsv"/>
116 <param name="input_metadata" value="HMP2_metadata.tsv"/> 156 <param name="input_metadata" value="HMP2_metadata.tsv"/>
117 <param name="random_effects" value="site,subject"/> 157 <param name="random_effects" value= "2,5"/>
118 <param name="fixed_effects" value="diagnosis,dysbiosisnonIBD,dysbiosisUC,dysbiosisCD,antibiotics,age"/> 158 <param name="fixed_effects" value="4,9,10,11,6,3"/>
159 <param name="reference" value="diagnosis,nonIBD"/>
119 <section name="additional_options"> 160 <section name="additional_options">
120 <param name="min_abundance" value="0.0"/> 161 <param name="min_abundance" value="0.0"/>
121 <param name="min_prevalence" value="0.1"/> 162 <param name="min_prevalence" value="0.1"/>
122 <param name="max_significance" value="0.25"/> 163 <param name="max_significance" value="0.25"/>
123 <param name="normalization" value="NONE"/> 164 <param name="normalization" value="NONE"/>
130 <param name="plot_heatmap" value="true"/> 171 <param name="plot_heatmap" value="true"/>
131 <param name="heatmap_first_n" value="50"/> 172 <param name="heatmap_first_n" value="50"/>
132 <param name="plot_scatter" value="true"/> 173 <param name="plot_scatter" value="true"/>
133 <param name="residuals_output" value="true"/> 174 <param name="residuals_output" value="true"/>
134 </section> 175 </section>
176 <output name="archive_output">
177 <assert_contents>
178 <has_size value="15005328" delta="1000000" />
179 </assert_contents>
180 </output>
135 <output name="all_results"> 181 <output name="all_results">
136 <assert_contents> 182 <assert_contents>
137 <has_text text="feature"/> 183 <has_text text="feature"/>
138 <has_n_lines n="610"/> 184 <has_n_lines n="610"/>
139 <has_n_columns n="9"/> 185 <has_n_columns n="9"/>
140 </assert_contents> 186 </assert_contents>
141 </output> 187 </output>
142 <output name="significant_results"> 188 <output name="significant_results">
143 <assert_contents> 189 <assert_contents>
144 <has_text text="dysbiosisCD"/> 190 <has_text text="dysbiosisCD"/>
145 <has_n_lines n="159"/> 191 <has_n_lines n="159" delta="10"/>
146 <has_n_columns n="9"/> 192 <has_n_columns n="9"/>
147 </assert_contents> 193 </assert_contents>
148 </output> 194 </output>
149 <output name="residuals"> 195 <output name="residuals">
150 <assert_contents> 196 <assert_contents>
151 <has_size value="462746" delta="1000"/> 197 <has_size value="462386" />
152 </assert_contents> 198 </assert_contents>
153 </output> 199 </output>
154 <output name="headmap"> 200 <output name="headmap">
155 <assert_contents> 201 <assert_contents>
156 <has_size value="7373" delta="1000" /> 202 <has_size value="7373" delta="1000" />
192 <has_size value="1037005" delta="1000000" /> 238 <has_size value="1037005" delta="1000000" />
193 </assert_contents> 239 </assert_contents>
194 </element> 240 </element>
195 </output_collection> 241 </output_collection>
196 </test> 242 </test>
197 <test expect_num_outputs="5"> 243 <test expect_num_outputs="6">
198 <param name="input_data" value="HMP2_taxonomy.tsv"/> 244 <param name="input_data" value="HMP2_taxonomy.tsv"/>
199 <param name="input_metadata" value="HMP2_metadata.tsv"/> 245 <param name="input_metadata" value="HMP2_metadata.tsv"/>
200 <param name="fixed_effects" value="diagnosis,dysbiosisnonIBD"/> 246 <param name="fixed_effects" value="4,9"/>
247 <param name="reference" value="diagnosis,nonIBD"/>
201 <section name="additional_options"> 248 <section name="additional_options">
202 <param name="min_abundance" value="0.0"/> 249 <param name="min_abundance" value="0.0"/>
203 <param name="min_prevalence" value="0.1"/> 250 <param name="min_prevalence" value="0.1"/>
204 <param name="max_significance" value="0.25"/> 251 <param name="max_significance" value="0.25"/>
205 <param name="normalization" value="NONE"/> 252 <param name="normalization" value="NONE"/>
212 <param name="plot_heatmap" value="true"/> 259 <param name="plot_heatmap" value="true"/>
213 <param name="heatmap_first_n" value="50"/> 260 <param name="heatmap_first_n" value="50"/>
214 <param name="plot_scatter" value="true"/> 261 <param name="plot_scatter" value="true"/>
215 <param name="residuals_output" value="true"/> 262 <param name="residuals_output" value="true"/>
216 </section> 263 </section>
264 <output name="archive_output">
265 <assert_contents>
266 <has_size value="12630049" delta="1000000" />
267 </assert_contents>
268 </output>
217 <output name="all_results"> 269 <output name="all_results">
218 <assert_contents> 270 <assert_contents>
219 <has_text text="feature"/> 271 <has_text text="feature"/>
220 <has_n_lines n="262"/> 272 <has_n_lines n="262"/>
221 <has_n_columns n="9"/> 273 <has_n_columns n="9"/>
222 </assert_contents> 274 </assert_contents>
223 </output> 275 </output>
224 <output name="significant_results"> 276 <output name="significant_results">
225 <assert_contents> 277 <assert_contents>
226 <has_text text="diagnosis"/> 278 <has_text text="diagnosis"/>
227 <has_n_lines n="175"/> 279 <has_n_lines n="175" delta="5"/>
228 <has_n_columns n="9"/> 280 <has_n_columns n="9"/>
229 </assert_contents> 281 </assert_contents>
230 </output> 282 </output>
231 <output name="residuals"> 283 <output name="residuals">
232 <assert_contents> 284 <assert_contents>
233 <has_size value="367224" delta="1000"/> 285 <has_size value="366875"/>
234 </assert_contents> 286 </assert_contents>
235 </output> 287 </output>
236 <output_collection name="figures_pdfs" type="list"> 288 <output_collection name="figures_pdfs" type="list">
237 <element name="diagnosis.pdf" ftype="pdf"> 289 <element name="diagnosis.pdf" ftype="pdf">
238 <assert_contents> 290 <assert_contents>
239 <has_size value="6234127" delta="1000000" /> 291 <has_size value="6234127" delta="1000000" />
240 </assert_contents> 292 </assert_contents>
241 </element> 293 </element>
242 </output_collection> 294 </output_collection>
243 </test> 295 </test>
244 <test expect_num_outputs="5"> 296 <test expect_num_outputs="6">
245 <param name="input_data" value="HMP2_taxonomy.tsv"/> 297 <param name="input_data" value="HMP2_taxonomy.tsv"/>
246 <param name="input_metadata" value="HMP2_metadata.tsv"/> 298 <param name="input_metadata" value="HMP2_metadata.tsv"/>
247 <param name="fixed_effects" value="diagnosis,dysbiosisnonIBD"/> 299 <param name="fixed_effects" value="2,4"/>
300 <param name="reference" value="site,Cedars-Sinai,diagnosis,UC"/>
248 <section name="additional_options"> 301 <section name="additional_options">
249 <param name="min_abundance" value="0.0001"/> 302 <param name="min_abundance" value="0.0001"/>
250 <param name="min_prevalence" value="0.1"/> 303 <param name="min_prevalence" value="0.1"/>
251 <param name="max_significance" value="0.25"/> 304 <param name="max_significance" value="0.25"/>
252 <param name="normalization" value="NONE"/> 305 <param name="normalization" value="NONE"/>
259 <param name="plot_heatmap" value="true"/> 312 <param name="plot_heatmap" value="true"/>
260 <param name="heatmap_first_n" value="50"/> 313 <param name="heatmap_first_n" value="50"/>
261 <param name="plot_scatter" value="true"/> 314 <param name="plot_scatter" value="true"/>
262 <param name="residuals_output" value="true"/> 315 <param name="residuals_output" value="true"/>
263 </section> 316 </section>
317 <output name="archive_output">
318 <assert_contents>
319 <has_size value="18278259" delta="1000000" />
320 </assert_contents>
321 </output>
264 <output name="all_results"> 322 <output name="all_results">
265 <assert_contents> 323 <assert_contents>
266 <has_text text="feature"/> 324 <has_text text="feature"/>
267 <has_n_lines n="250"/> 325 <has_n_lines n="415" delta="10"/>
268 <has_n_columns n="9"/> 326 <has_n_columns n="9"/>
269 </assert_contents> 327 </assert_contents>
270 </output> 328 </output>
271 <output name="significant_results"> 329 <output name="significant_results">
272 <assert_contents> 330 <assert_contents>
273 <has_text text="diagnosis"/> 331 <has_text text="diagnosis"/>
274 <has_n_lines n="172"/> 332 <has_n_lines n="300" delta="15"/>
275 <has_n_columns n="9"/> 333 <has_n_columns n="9"/>
276 </assert_contents> 334 </assert_contents>
277 </output> 335 </output>
278 <output name="residuals"> 336 <output name="residuals">
279 <assert_contents> 337 <assert_contents>
280 <has_size value="359943" delta="1000"/> 338 <has_size value="363118"/>
281 </assert_contents> 339 </assert_contents>
282 </output> 340 </output>
283 <output name="headmap"> 341 <output name="headmap">
284 <assert_contents> 342 <assert_contents>
285 <has_size value="6554" delta="1000" /> 343 <has_size value="7000" delta="1000" />
286 </assert_contents> 344 </assert_contents>
287 </output> 345 </output>
288 <output_collection name="figures_pdfs" type="list"> 346 <output_collection name="figures_pdfs" type="list">
289 <element name="heatmap.pdf" ftype="pdf"> 347 <element name="heatmap.pdf" ftype="pdf">
290 <assert_contents> 348 <assert_contents>
291 <has_size value="6554" delta="1000" /> 349 <has_size value="7693" delta="100" />
292 </assert_contents> 350 </assert_contents>
293 </element> 351 </element>
294 <element name="diagnosis.pdf" ftype="pdf"> 352 <element name="diagnosis.pdf" ftype="pdf">
295 <assert_contents> 353 <assert_contents>
296 <has_size value="6061545" delta="1000000" /> 354 <has_size value="6061545" delta="1000000" />
297 </assert_contents> 355 </assert_contents>
298 </element> 356 </element>
299 <element name="dysbiosisnonIBD.pdf" ftype="pdf"> 357
300 <assert_contents>
301 <has_size value="2599373" delta="1000000" />
302 </assert_contents>
303 </element>
304 </output_collection> 358 </output_collection>
305 </test> 359 </test>
360 <test expect_num_outputs="6">
361 <param name="input_data" value="HMP2_taxonomy.tsv"/>
362 <param name="input_metadata" value="HMP2_metadata.tsv"/>
363 <param name="fixed_effects" value="7,9"/>
364 <param name="random_effects" value="3" />
365
366 <section name="additional_options">
367 <param name="min_abundance" value="0.0"/>
368 <param name="min_prevalence" value="0.1"/>
369 <param name="max_significance" value="0.25"/>
370 <param name="normalization" value="TSS"/>
371 <param name="transform" value="LOG"/>
372 <param name="analysis_method" value="LM"/>
373 <param name="correction" value="BY"/>
374 <param name="standardize" value="True"/>
375 </section>
376 <section name="output">
377 <param name="plot_heatmap" value="true"/>
378 <param name="heatmap_first_n" value="50"/>
379 <param name="plot_scatter" value="true"/>
380 <param name="residuals_output" value="true"/>
381 </section>
382 <output name="archive_output">
383 <assert_contents>
384 <has_size value="8567935" delta="1000000" />
385 </assert_contents>
386 </output>
387 <output name="all_results">
388 <assert_contents>
389 <has_text text="feature"/>
390 <has_n_lines n="175" delta="10"/>
391 <has_n_columns n="9"/>
392 </assert_contents>
393 </output>
394 <output name="significant_results">
395 <assert_contents>
396 <has_text text="dysbiosisnonIBD"/>
397 <has_n_lines n="95" delta="5"/>
398 <has_n_columns n="9"/>
399 </assert_contents>
400 </output>
401 <output name="residuals">
402 <assert_contents>
403 <has_size value="434087"/>
404 </assert_contents>
405 </output>
406 <output_collection name="figures_pdfs" type="list">
407 <element name="heatmap.pdf" ftype="pdf">
408 <assert_contents>
409 <has_size value="7000" delta="1000" />
410 </assert_contents>
411 </element>
412 </output_collection>
413 </test>
414
415
306 </tests> 416 </tests>
307 <help><![CDATA[ 417 <help><![CDATA[
308 @HELP_HEADER@ 418 @HELP_HEADER@
309 MaAsLin 2 419 MaAsLin 2
310 ========= 420 =========
344 - Q-values smaller than or equal to the threshold (tabular file) 454 - Q-values smaller than or equal to the threshold (tabular file)
345 - This file is a subset of the results in the first file. 455 - This file is a subset of the results in the first file.
346 - It only includes associations with q-values <= to the threshold. 456 - It only includes associations with q-values <= to the threshold.
347 - Data frame with residuals for each feature (R data file) 457 - Data frame with residuals for each feature (R data file)
348 - This file contains a data frame with residuals for each feature. 458 - This file contains a data frame with residuals for each feature.
459
460 Correction methods to compute the q-value : https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/p.adjust
461
349 2- Visualization output files 462 2- Visualization output files
350 - Heatmap of the significant associations (PDF file) 463 - Heatmap of the significant associations (PDF file)
351 - This file contains a heatmap of the significant associations. 464 - This file contains a heatmap of the significant associations.
352 - A plot for every significant association found (PDF file(s)) 465 - A plot for every significant association found (PDF file(s))
353 - A plot is generated for each significant association. 466 - A plot is generated for each significant association.