LBMC » NucleoMiner

# built documents.

#

# The short X.Y version.

# The full version, including alpha/beta/rc tags.

# The language for content autogenerated by Sphinx. Refer to documentation

# for a list of supported languages.

::

Arguments

~~~~~~~~~

::

    align_inter_strain_nucs(replicates, wp_nucs_strain_ref1 = NULL, 

        config = NULL, ...)

Arguments

+---------------+---------------------------------------------------+

| Author:       | Florent Chuffart                                  |

+---------------+---------------------------------------------------+

+---------------+---------------------------------------------------+

| License:      | CeCILL                                            |

+---------------+---------------------------------------------------+

        plot_gaussian_unified_reads = TRUE, plot_ellipse_nucs = TRUE, 

        plot_wp_nucs = TRUE, plot_wp_nuc_model = TRUE, plot_common_nucs = TRUE, 

        plot_anovas = FALSE, plot_anova_boxes = FALSE, plot_wp_nucs_4_nonmnase = FALSE, 

Arguments

~~~~~~~~~

Plot (or not) clusters for non inputs samples.

``aggregated_intra_strain_nucs``

list of aggregated intra strain nucs. If NULL, it will be computed.

Package: nucleominer

Maintainer: Florent Chuffart <florent.chuffart@ens-lyon.fr>

Author: Florent Chuffart

License: CeCILL 

Title: nm

Depends: seqinr, plotrix, DESeq, cachecache

  llX = sum(log(dnorm(x,mean=meanX,sd=sdX)))

  llY = sum(log(dnorm(y,mean=meanY,sd=sdY)))

  llXY = sum(log(dnorm(c(x,y),mean=meanXY,sd=sdXY)))

  return(ratio)

### Returns the likelihood ratio.

}, ex=function(){

aggregate_intra_strain_nucs = structure(function(# Aggregate replicated sample's nucleosomes. 

### This function aggregates nucleosome for 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 \emph{lod_scores}. Each cluster ows an attribute \emph{wp} for "well positionned". This attribute is set as \emph{TRUE} if the cluster is composed of exactly one nucleosomes of each sample.

samples, ##<< A list of samples. Each sample is a list like \emph{sample = list(id=..., marker=..., strain=..., roi=..., inputs=..., outputs=...)} with \emph{roi = list(name=..., begin=...,  end=..., chr=..., genome=...)}.

coord_max=20000000 ##<< A too big value to be a coord for a nucleosome lower bound.

){

	end_of_tracks = function(tracks) {

  indexes = c()

  track_readers = c()

  current_nuc = NULL

  # Read nucs from TF outputs  

  tf_outs = list()

	i = 1

		}

		# print(paste(lod_score, length(current_nuc$original_reads), length(new_nuc$original_reads), sep=" "))

		if (is.na(lod_score)) {

		}

      # aggregate to current cluster

      #   update bound

      if (new_nuc$upper_bound > new_cluster$upper_bound) {

wp_nucs_strain_ref1=NULL, ##<< List of aggregates nucleosome for strain 1. If it's null this list will be computed.

wp_nucs_strain_ref2=NULL, ##<< List of aggregates nucleosome for strain 2. If it's null this list will be computed.

corr_thres=0.5, ##<< Correlation threshold.

config=NULL, ##<< GLOBAL config variable

... ##<< A list of parameters that will be passed to \emph{aggregate_intra_strain_nucs} if needed.	

) {

								lod_score = lod_score_vecs(reads_strain_ref1, reads_strain_ref2)

								lod_scores = c(lod_scores, lod_score)

								# Filtering on LOD Score						

									tmp_nuc = list()

									# strain_ref1

									tmp_nuc[[paste("chr_", strain_ref1, sep="")]] = chr

		}

	}

	print(length(rois_3rd_round[,1]))

	print(sum(rois_3rd_round$length))

	rois = rois_3rd_round

plot_anovas = FALSE,  ##<< Plot (or not) scatter for each nuc.

plot_anova_boxes =  FALSE,  ##<< Plot (or not) boxplot for each nuc.

plot_wp_nucs_4_nonmnase = FALSE,  ##<< Plot (or not) clusters for non inputs samples.

aggregated_intra_strain_nucs = NULL, ##<< list of aggregated intra strain nucs. If NULL, it will be computed. 

aligned_inter_strain_nucs = NULL, ##<< list of aligned inter strain nucs. If NULL, it will be computed.

height = 10, ##<< Number of reads in per million read for each sample, graphical parametre for the y axis.

		    }

			}

	  }

	  # Plot wp nucs

			if (samples[[1]]$marker == "Mnase_Seq") {

				if (is.null(aggregated_intra_strain_nucs)) {

	  			wp_nucs = aggregate_intra_strain_nucs(samples)[[1]]			

				} else {

					wp_nucs = aggregated_intra_strain_nucs[[replicate_rank]]

				}

		  } else {

  			wp_nucs = replicates_wp_nucs[[replicate_rank-2]]

		  }

		}

	}