Mercurial > repos > qfabrepo > metadegalaxy_phyloseq_deseq2

annotate phyloseq_2_deseq2.r @ 1:a55b89bc9788 draft

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"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 9767e7d8ab085c7d6323b8323d9047cb68bc0211"
author qfabrepo
date Wed, 16 Sep 2020 06:34:40 +0000
parents 1f0569e94be4
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1 library('getopt')
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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2 suppressPackageStartupMessages(library('phyloseq'))
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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3 suppressPackageStartupMessages(library('DESeq2'))
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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5 options(warn= -1)
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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7 option_specification = matrix(c(
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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8 'biomfile','b',2,'character',
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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9 'metafile','m',2,'character',
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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10 'factor','f',2,'numeric',
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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11 'test','t',2,'character',
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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12 'fitType','T',2,'character',
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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13 'cutoff','c','2','double',
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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14 'outdir','o',2,'character',
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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15 'result','r',2,'character',
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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16 'normalisedResult','n','2','character'
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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17 ),byrow=TRUE,ncol=4);
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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20 options <- getopt(option_specification);
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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21 options(bitmapType="cairo")
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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24 if (!is.null(options$outdir)) {
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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25 # Create the directory
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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26 dir.create(options$outdir,FALSE)
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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27 }
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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30 galaxy_biom <- import_biom(options$biomfile)
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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31 galaxy_map <- import_qiime_sample_data(options$metafile)
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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32 tax_col_norm <- c("Kingdom","Phylum","Class","Order","Family","Genus","Species")
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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33 tax_col_extra <- c("None","Kingdom","Phylum","Class","Order","Family","Genus","Species")
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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35 number.of.tax.rank<-length(colnames(tax_table(galaxy_biom)))
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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37 if( number.of.tax.rank == 7){
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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38 colnames(tax_table(galaxy_biom)) <- tax_col_norm
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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39 }else{
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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40 colnames(tax_table(galaxy_biom)) <- tax_col_extra
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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41 }
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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44 AIP_galaxy <- merge_phyloseq(galaxy_biom,galaxy_map)
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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47 Infactor<-colnames(galaxy_map)[options$factor]
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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48 method<-options$test
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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49 Type<-options$fitType
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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50 cutoff<-options$cutoff
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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54 suppressMessages(deseq2_obj<-phyloseq_to_deseq2(AIP_galaxy,as.formula(paste('~',Infactor,sep=""))))
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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55 gm_mean = function(x, na.rm=TRUE){
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56 exp(sum(log(x[x > 0]), na.rm=na.rm) / length(x))
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57 }
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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58 geoMeans = apply(counts(deseq2_obj), 1, gm_mean)
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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59 deseq2_obj = estimateSizeFactors(deseq2_obj, geoMeans = geoMeans)
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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63 ### Normalisation
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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64 deseq2_obj_norm<-counts(deseq2_obj,normalized=T)
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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65 deseq2_obj_norm.out<-as.data.frame(cbind("OTUID"=rownames(deseq2_obj_norm),deseq2_obj_norm))
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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66 write.table(deseq2_obj_norm.out,file=options$normalisedResult,col.names=T,row.names=F,quote=F,sep="\t")
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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69 ### Normalisation and DE analysis
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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70 suppressMessages(deseq2_obj_DE<-DESeq(deseq2_obj,test=method,fitType=Type))
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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71 res = results(deseq2_obj_DE,cooksCutoff = FALSE)
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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73 significant.table <-res[which(res$padj < cutoff),]
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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75 if(nrow(significant.table) == 0){
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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76 out_message <-"no significant result found!"
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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77 write(out_message,file=options$result,sep="\t")
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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78 quit("yes")
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79 }
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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81 significant.table <- cbind(as(significant.table,"data.frame"), as(tax_table(AIP_galaxy)[rownames(significant.table),],"matrix"))
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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83 significant.table.out<-as.data.frame(cbind("OTUID"=rownames(significant.table),significant.table))
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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85 write.table(format(significant.table.out, digits=4, scientific=F),file=options$result,col.names=T,row.names=F,quote=F,sep="\t")
1f0569e94be4 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_2_deseq2 commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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