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Analyzed about 1 year ago. based on code collected about 1 year ago.
Jan 18, 2023 — Jan 18, 2024
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
Create README.md
Xavier de Pedro Puente
More... almost 9 years ago
Anonymized old version of basicA.Rmd and clean it a bit.
Xavier de Pedro Puente
as xavidp
More... about 9 years ago
Anonymized a bit more basicA.R
Xavier de Pedro Puente
as xavidp
More... about 9 years ago
Added .gitignore files
Xavier de Pedro Puente
as xavidp
More... about 9 years ago
Ignored .bzr folders and theri contents
Xavier de Pedro Puente
as xavidp
More... about 9 years ago
Renamed project locally
Xavier de Pedro Puente
as xavidp
More... about 9 years ago
Merge branch 'master' of github.com:xavidp/bpmmirna First commit after merging the empty project in github with the local history tree exported from bazaar to git.
Xavier de Pedro Puente
as xavidp
More... about 9 years ago
removed .bzrignore
Xavier de Pedro Puente
as xavidp
More... about 9 years ago
Initial commit
Xavier de Pedro Puente
More... about 9 years ago
basicA.R * added logs folder to store output from linklint, for instance, nowadays, and eventually other output (R profile info, session info, etc) * fixed naming of file annotation.affy.hg.fileName.noext (from featureAnotation to featureAnnotation) * csv file featureAnotation.csv created also when data doesn't come from DataPreprocessing.R but from Expression Console * Logic added to Check that there are no broken links in the report (using linklink gnu/linux system package) * Logic added to Pack the report into a zip file in the baseDir * Place holder and tips added to Send the ftp file to the VHIR ftp for the researcher * SessionInfo and Valid packages stored in the logs folder
Xavier de Pedro
More... about 9 years ago
basicA.R: * added googleVis to generate table with colors for the targets file (targets.all.colored.html; to match the colors in the plots for each group, etc) * added the analysis title and date of report in the first part of the report. * added study budget file in the Main Documents section. * filter input data set to remove non human data and controls. Cleaned source data for putative gene report: data.p.genes * indicate that key.parms aer also used for the putative gene report. * change color of highlighted rows in numFeaturesChanged from red (isSignificant=TRUE) to blue (isSignificant=FALSE) * added function volcanoplot2, which is just a clon of volcanoplot from limma, but trimming labels from 15 onwards, and not just from 8 characters. this allows for labels to display the full name of ProbeSetNames * Fix vulcanoPointNames: avoid doing a risky merge (which changes order), but use the equivalent column in data.p.genes for "Transcript ID(Array Design)". * Added the section in the report to display the Potentially Regualated Genes, one csv file for each comparison. * added images to the report: vhir and ueb logos at the header-like section, and an image at the footer-like section.
Xavier de Pedro
More... about 9 years ago
basicA.R: * Added a new section in the report, as place holder, for the Genes potentially regulated by miRNA , with bulk data as csv for a computational start. ToDo: calculate the tables genRegTab properly. * replaced the "Made with Nozzle" in teh Report html with "Made with R" (and updating the link, accordingly). * implemented logic to detect rows.selected.idx (to highlight rows in the numFeaturesChanged) depenting on the values set as pValcutoff and AdjuMethod (stored in key.params). Works for cases with same condition to all comparisons. ToDo: allow different params among comparisons.
Xavier de Pedro
More... about 9 years ago
basicA.R: * Added a few cross references and some key.params are included in the report. * rows in numFeaturesChanged corresponding to the chosen parameters (pValcutoff, etc) are highlighted .
Xavier de Pedro
More... about 9 years ago
basicA.R: * Improved look and feel of subsections (treated as subsections and not as sections when they were expected to be a lower level in styles) * fixed order of comparisons (AvsB = A - B) * highlighted in another color the samples2remove * added comments on how to attempt to produce the volcano plot as an interactive svg chart
Xavier de Pedro
More... about 9 years ago
basicA.R: * fixed tex tables to be used in the Rnw for the proposal * fixed conditions splitted by "vs" when each comparison set has more than one comparison * added compGroupName descriptions to the object passed to the Rnw for the proposal
Xavier de Pedro
More... about 9 years ago
basicA.R: * splitted doQC into doQCPlots and doQCCustomRaw or doQCCustomNorm, or doQCBiocRaw or doQCBiocNorm. So there is a higher degree or code reuse to make similar QC with all samples or with all minus samples to be removed (as indicated in samples2remove) * Addapted report chunks handling to fit selection of QC types (finished for doQCCustom*, but missing still for doQCBioc*. * Added comments on how to implement one day the VolcanoPlots in svg so that it's easier to identify points in the chart and provide it's metadata (Sample, Group, etc)
Xavier de Pedro
More... about 9 years ago
basicA.R * Fixed algorythm to properly handle subset of data (targets, expression sets, sampleNames-Colors-Shortnames-Grupo) after removing the sample names indicated in the param samples2remove (after QC info).
Xavier de Pedro
More... about 9 years ago
* Added d3.v3.js and dimple.v2.1.0.js for the svg version of the pca files from QC custom code (plotPCAsvg).
Xavier de Pedro
More... about 9 years ago
* Added usage of R packages parallel and xtable, etc. Saving tex chunks on disk * QCPlots: make png's instead of showin them in the graphic device and refactor QCPlots naming (for pdf and png) * set number of cores max -1 * save Rda on disk to be reused at the Rnw level * add Rnw for the proposal under revision control
Xavier de Pedro
More... about 9 years ago
Added missing latex includes so that typing accents in Spanish works by default (ubuntu system packages need to be updated using some extra packages, see http://ueb.vhir.org/14.04 )
Xavier de Pedro
More... about 9 years ago
Added generic study proposal in tex (docs/yyyy-mm-NameSurname-CENTER-StudyProposal.tex) , borrowed from the stanrdard Basic-Pipe package (thanks Miriam), sync'ed from version 197 from that repo.
Xavier de Pedro
More... about 9 years ago
* Minor comment added to basicA.R (about what to do when some samples are removed from the anaylisis based on QC output info). * First version of the Rmd equivalent (basicA.Rmd).
Xavier de Pedro
More... about 9 years ago
dades/rma.XXXNNN.ec.annotated.txt: * added as a reference of file produced by Expression Console with annotation info.
Xavier de Pedro
More... about 9 years ago
DataPreprocessing.R: * Added section titles (commented out) * refactored name rma_affy_annotated_ref.txt into rma.affy.annotated.ref.txt * refactored internal object names as well s Rda sav ed on disk to have higher degree of consistency (and more intuitive) * cdf package name reset by default to mirna40cdf * identified more clearly the 2 source processes to generate normalized data (from rma Expression console data OR from vsnrma converted through Bioconductor-generated rawData) * selection of human mirnas and removal of controls moved from basicA.R to DataPreprocessing.R * more objects saved into Rda on disk (still many need to be optioanlly read from basicA.R; todo) * rawData (former object xx) was rewritten into the same object the second time it was generated (mking useless the first time it was generated) * arrayQualityMetrics commented out from the Quality control over the raw data since it still crashes the R session * kept (even if commented out) the second way to calculate the numFeaturesChanged (from Alex's code)
Xavier de Pedro
More... about 9 years ago
* fixed wrong path for when loading data.normalized.aID.Rda * updated names of files Rda saved on disk
Xavier de Pedro
More... about 9 years ago
basicA.R: * do some testing of the usage of data.tables for merging, which seems to be up to 5 times more efficient than basic merge, even if it re-sorts values. therefore, for this pipeline, we leave the code commented out (for the time being, at least). * added reference to reports dir (rel and absolute) * Added a note to remember to tweak the contrasts matrix also when you remove some samples from the analysis (after QC reports) * Replace Probe.Set.Names with Transcript_IDs in ** volcanoPlot point names ** list of features found in each section of Venn diagrams (stored in csv files): listVenn.tid. We keep also the object lisVenn.psn because we need them for the HeatMaps to filter the expression set on probesetnames. ** Heatmaps updated * report phase 4 coded: ** js and css files are copied from reports folder to results folder, if they are missing, at the end of each run ** the resulting html and checked against the absolute url of datatables package, and removed the absolute path to leave only relative paths that will work when the results folder is sent elsewhere to the researchers to view his results.
Xavier de Pedro
More... about 9 years ago
* folder names renamed to english and abstracted with a param * added analysisName as param, as well as analysis ID (aID) in a few places to avoid re-writing the same code by hand too much * add checks to run the code to remove samples only if there are samples to remove (oltherwise, some artifacts were generated in some cases) * tweaked by hand the cdf version from mirna40cdf to mirna41cdf. * added the files required for cdf package to be constructed (miRNA-4_0-st-v1.cdf and miRNA-4_0-st-v1.psi) * samples2remove pre-set to zero by defult, while keeping an example commented out * design matrix: colnames are rewritten only for the ones not related to batch effects * new splitterIntracond parameter to help the code find out which sub strings are to be searched for as conditions in the names of comparisons. ** used in my.conds.units and my.cels.idx, to have the heatmap generation code again as expected. * pValCutOff, adjMethod and minLogFoldChange are created by default as repeated values for as many times as comparison groups. * Quality control chunk fully commented out for raw Data, and uncommented out for normalized data, even if it fails still at some point (general crash for raw Data before producing any output, and in the middle of the output for norm data) * removed hardcoding "ColoresTipoT" as column in pData(exprs.filtered) and set as "Colores" again * added acknowledgement section as "Other considerations" in the report * renamed template reports/BRB279.Rnw as reports/XXXNNN.Rnw
Xavier de Pedro
More... about 9 years ago
* anonymized a little bit more
Xavier de Pedro
More... about 9 years ago
* added dades/rma_affy_annotated_ref.txt which contains the list of: Probe_Set_ID Species_Scientific_Name Sequence Type Sequence Source Transcript_ID Probe Set Name from affymetrix, which will be used to annotate the expression values corresponding to the probesets in the rma.XXXNNN.summary.txt
Xavier de Pedro
More... about 9 years ago
* File names refactoring: PreparaDades.A279.R -> DataPreprocessing.R * Removed unused file (as separated script) Rcode/venn_from_distinct.A279.R * added sample dades/rma.XXXNNN.summary.txt as a reference file needed, generated by the wetlab analyst
Xavier de Pedro
More... about 9 years ago