/doc/sphinx_doc/rref.rst - Diff - NucleoMiner - Forge du Centre Blaise Pascal

Révision e5603c3f doc/sphinx_doc/rref.rst

     Description
     ~~~~~~~~~~~
     Util to convert Arabicto Roman
     Utility to convert Arabic numbers to Roman numbers
     Usage
     ~~~~~
-...
     Description
     ~~~~~~~~~~~
     Util to convert Roman to Arabic
     Utility to convert Roman numbers into Arabic numbers
     Usage
     ~~~~~
-...
     Description
     ~~~~~~~~~~~
     This function aggregates nucleosome for replicated samples. It uses
     This function aggregates nucleosomes from replicated samples. It uses
     TemplateFilter ouput of each sample as replicate. Each sample owns a set
     of nucleosomes computed using TemplateFilter and ordered by the position
     of their center. Adajacent nucleosomes are compared two by two.
     Comparison is based on a log likelihood ratio score. The issue of
     comparison is adjacents nucleosomes merge or separation. Finally the
     function returns a list of clusters and all computed *llr\_scores*. Each
     cluster ows an attribute *wp* for "well positionned". This attribute is
     set as *TRUE* if the cluster is composed of exactly one nucleosomes of
     each sample.
     of their center (dyad). A chain of nucleosomes is builts across all
     replicates. Adjacent nucleosomes of the chain are compared two by two.
     Comparison is based on a log likelihood ratio (LLR1). depending on the
     LLR1 value nucleosomes are merged (low LLR) or separated (high LLR).
     Finally the function returns a list of clusters and all computed
     llr\_scores. Each cluster ows an attribute wp for “well positioned”.
     This attribute is set to TRUE if the cluster is composed of exactly one
     nucleosome of each sample.
     Usage
     ~~~~~
-...
     ``llr_thres``
     Log likelihood ration threshold.
     Log likelihood ratio threshold to decide between merging and separating
     ``coord_max``
-...
     Description
     ~~~~~~~~~~~
     This function aligns nucs between two strains for a given genome region.
     This function aligns nucleosomes between two strains for a given genome
     region.
     Usage
     ~~~~~
-...
     ``wp_nucs_strain_ref1``
     List of aggregates nucleosome for strain 1. If it's null this list will
     List of aggregates nucleosome for strain 1. If it's NULL this list will
     be computed.
     ``wp_nucs_strain_ref2``
     List of aggregates nucleosome for strain 2. If it's null this list will
     List of aggregates nucleosome for strain 2. If it's NULL this list will
     be computed.
     ``corr_thres``
-...
     ``llr_thres``
     LOD cut off.
     Log likelihood ratio threshold to decide between merging and separating
     ``config``
-...
+        }
         print(align_inter_strain_nucs(replicates))
     R: Launch deseq methods.
     R: Launch DESeq methods.
     Launch deseq methods.
     Launch DESeq methods.
     ---------------------
     Description
     ~~~~~~~~~~~
     This function is based on deseq example. It mormalizes data, fit data to
     GLM model with and without interaction term and compare the two
     l;=models.
     This function is based on DESeq example. It normalizes data, fit data to
     GLM model with and without interaction term and compares the two models.
     Usage
     ~~~~~
-...
     ``snep_design``
     The design to considere.
     The design to consider.
     ``reads``
     The data to considere.
     The data to consider.
     Author(s)
     ~~~~~~~~~
-...
     Description
     ~~~~~~~~~~~
     This function loads in memory data corresponding to the given
     This function loads in memory the data corresponding to the given
     experiments.
     Usage
-...
     ``expe``
     a list of vector corresponding to vector of replicates.
     a list of vectors corresponding to replicates.
     ``roi``
-...
         # library(nucleominer)
+        #
         # # Read config file
         # json_conf_file = "nucleo_miner_config.json"
         # json_conf_file = "nucleominer_config.json"
         # config = fromJSON(paste(readLines(json_conf_file), collapse=""))
         # # Read sample file
         # all_samples = get_content(config$CSV_SAMPLE_FILE, "cvs", sep=";", head=TRUE, stringsAsFactors=FALSE)
-...
     Description
     ~~~~~~~~~~~
     This fonction allow to acces to a specific part of the c2c file.
     This fonction allows to access to a specific part of the c2c file.
     Usage
     ~~~~~
-...
     ``chr``
     if defined, the c2c will filtered according to the chromosome value
     if defined, the c2c will be filtered according to the chromosome value
     ``lower_bound``
     if defined, the c2c will filtered for part of the genome upper than
     if defined, the c2c will be filtered for part of the genome upper than
     lower\_bound
     ``upper_bound``
     if defined, the c2c will filtered for part of the genome lower than
     if defined, the c2c will be filtered for part of the genome lower than
     upper\_bound
     ``config``
-...
     Florent Chuffart
     R: Build the design for deseq
     R: Build the design for DESeq
     Build the design for deseq
     Build the design for DESeq
     --------------------------
     Description
-...
     ::
         get_sneps(marker, combi, form, all_samples, config = NULL)
         get_sneps(marker, combi, form, all_samples, FDR = 1e-04, config = NULL)
     Arguments
     ~~~~~~~~~
-...
     Global list of samples.
     ``FDR``
     ``config``
     GLOBAL config variable
-...
     ::
         # LOD score for 2 set of values
         # LLR score for 2 set of values
         mean1=5; sd1=2; card2 = 250
         mean2=6; sd2=3; card1 = 200
         x1 = rnorm(card1, mean1, sd1)
-...
     Description
     ~~~~~~~~~~~
     This fuxntion use the deseq nomalization feature to compare
     This fuxntion use the DESeq nomalization feature to compare
     qualitatively the distribution.
     Usage
-...
     Description
     ~~~~~~~~~~~
     This function is an eloborated call to translate\_cur.
     This function is an elaborated call to translate\_cur.
     Usage
     ~~~~~
-...
     Florent Chuffart
     R: Aggregate regions that intersect themnselves.
     R: Aggregate regions that intersect themselves.
     Aggregate regions that intersect themnselves.
     ---------------------------------------------
     Aggregate regions that intersect themselves.
     --------------------------------------------
     Description
     ~~~~~~~~~~~

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LBMC » NucleoMiner

Révision e5603c3f doc/sphinx_doc/rref.rst