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+======
+edgepy
+======
+
+.. currentmodule:: inmoose.edgepy
+
+This module is a partial port in Python of the R Bioconductor `edgeR package
+<https://bioconductor.org/packages/release/bioc/html/edgeR.html>`_.
+Only the functionalities necessary to :func:`inmoose.pycombat.pycombat_seq` and
+differential expression analysis have been ported so far.
+
+Differential Expression Analysis Example
+========================================
+
+We give below an example of how to use :code:`edgepy` to perform a differential
+expression analysis on the pasilla dataset.
+
+.. repl::
+   from inmoose.data.pasilla import pasilla
+   from inmoose.edgepy import DGEList, glmLRT, topTags
+   from patsy import dmatrix
+
+   # load the pasilla dataset as an AnnData
+   pas = pasilla()
+
+   # extract the count matrix and the annotation dataframe from the AnnData object
+   counts = pas.X.T
+   anno = pas.obs
+   # build the design matrix
+   design = dmatrix("~condition", data=anno)
+
+   # build a DGEList object
+   dge_list = DGEList(counts=counts, samples=anno, group_col="condition", genes=pas.var)
+   # estimate the dispersions
+   dge_list.estimateGLMCommonDisp(design=design)
+
+   # fit the GLM
+   fit = dge_list.glmFit(design=design)
+
+   # run a differential expression analysis based on LRT
+   lrt = glmLRT(fit)
+
+   topTags(lrt)
+
+
+References
+==========
+
+.. [Chen2016] Y. Chen, A.T.L Lun, G.K. Smyth. 2016. From reads to genes to
+   pathways: differential expression analysis of RNA-Seq experiments using
+   Rsubread and the edgeR quasi-likelihood pipeline. *F1000Research* 5, 1438.
+   :doi:`10.12688/f1000research.8987.2`
+
+.. [Gibbons1975] J.D. Gibbons, J.W. Pratt. 1975. P-values: interpretation and
+   methodology. *The American Statistician* 29, 20-25.
+   :doi:`10.1080/00031305.1975.10479106`
+
+.. [Lun2016] A.T.L. Lun, Y. Chen, G.K. Smyth. 2016. It's DE-licious: a recipe
+   for differential expression analyses of RNA-seq experiments using
+   quasi-likelihood methods in edgeR.  *Methods in Molecular Biology* 1418,
+   391-416. :doi:`10.1007/978-1-4939-3578-9_19`
+
+.. [Lund2012] S.P. Lund, D. Nettleton, D.J. McCarthy, G.K. Smyth. 2012.
+   Detecting differential expression in RNA-sequence data using quasi-likelihood
+   with shrunken dispersion estimates. *Statistical Applications in Genetics and
+   Molecular Biology* Volume 11, Issue 5, Article 8.
+   :doi:`10.1515/1544-6115.1826`
+
+.. [Lun2017] A.T.L. Lun, G.K. Smyth. 2017. No counts, no variance: allowing for
+   loss of degrees of freedom when assessing biological variability from RNA-seq
+   data. *Statistical Applications in Genetics and Molecular Biology* 16(2),
+   83-93. :doi:`10.1515/sagmb-2017-0010`
+
+.. [McCarthy2012] D. J. McCarthy, Y. Chen, G. K. Smyth. 2012. Differential
+   expression analysis of multifactor RNA-Seq experiments with respect to
+   biological variation. Nucleic Acids Research 40, 4288-4297.
+   :doi:`10.1093/nar/gks042`
+
+.. [Phipson2016] B. Phipson, S. Lee, I.J. Majewski, W. S. Alexander, G.K. Smyth.
+   2016. Robust hyperparameter estimation protects against hypervariable genes
+   and improves power to detect differential expression. *Annals of Applied
+   Statistics* 10, 946-963. :doi:`10.1214/16-AOAS920`
+
+.. [Robinson2008] M.D. Robinson, g.K. Smyth. 2008. Small-sample estimation of
+   negative binomial dispersion, with applications to SAGE data.
+   *Biostatistics* 9, 321-332.  :doi:`10.1093/biostatistics/kxm030`
+
+
+Code documentation
+==================
+
+.. autosummary::
+   :toctree: generated/
+
+   DGEList
+
+   addPriorCount
+   adjustedProfileLik
+   aveLogCPM
+   binomTest
+   designAsFactor
+   dispCoxReid
+   dispCoxReidInterpolateTagwise
+   estimateGLMCommonDisp
+   estimateGLMTagwiseDisp
+   exactTest
+   exactTestBetaApprox
+   exactTestByDeviance
+   exactTestBySmallP
+   exactTestDoubleTail
+   glmFit
+   glmLRT
+   glmQLFit
+   glmQLFTest
+   mglmLevenberg
+   mglmOneGroup
+   mglmOneWay
+   movingAverageByCol
+   nbinomDeviance
+   plotQLDisp
+   predFC
+   splitIntoGroups
+   systematicSubset
+   topTags
+   validDGEList