LBMC » NucleoMiner

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

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.

Usage

~~~~~

Arguments

marker=..., strain=..., roi=..., inputs=..., outputs=...)* with *roi =

list(name=..., begin=..., end=..., chr=..., genome=...)*.

Log likelihood ration threshold.

Value

~~~~~

scores.

~~~~~

   align_inter_strain_nucs(replicates, wp_nucs_strain_ref1 = NULL,

       config = NULL, ...)

Correlation threshold.

LOD cut off.

Value

~~~~~

scores.

Description

~~~~~~~~~~~

Usage

~~~~~

Arguments

~~~~~~~~~

Value

~~~~~

Author(s)

   lines(min:max,dnorm(min:max,mean1,sd1)*card1,col=2)

   lines(min:max,dnorm(min:max,mean2,sd2)*card2,col=3)

   lines(min:max,dnorm(min:max,mean(c(x1,x2)),sd(c(x1,x2)))*card2,col=4)

R: nm

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

| Author:         | Florent Chuffart                                    |

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

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

| License:        | CeCILL                                              |

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

# 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.

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

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.

::

Arguments

~~~~~~~~~

marker=..., strain=..., roi=..., inputs=..., outputs=...)* with *roi =

list(name=..., begin=..., end=..., chr=..., genome=...)*.

Log likelihood ration threshold.

Value

~~~~~

Author(s)

~~~~~~~~~

::

    align_inter_strain_nucs(replicates, wp_nucs_strain_ref1 = NULL, 

        config = NULL, ...)

Arguments

Correlation threshold.

LOD cut off.

Value

~~~~~

Author(s)

~~~~~~~~~

Description

~~~~~~~~~~~

Usage

~~~~~

::

Arguments

~~~~~~~~~

Value

~~~~~

Author(s)

~~~~~~~~~

    lines(min:max,dnorm(min:max,mean1,sd1)*card1,col=2)

    lines(min:max,dnorm(min:max,mean2,sd2)*card2,col=3)

    lines(min:max,dnorm(min:max,mean(c(x1,x2)),sd(c(x1,x2)))*card2,col=4)

R: nm

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

| Author:       | Florent Chuffart                                  |

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

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

| License:      | CeCILL                                            |

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

Package: nucleominer

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

Author: Florent Chuffart

License: CeCILL 

Title: nm

Depends: seqinr, plotrix, DESeq, cachecache

(

) {

  return(ratio)

}, ex=function(){

  # LOD score for 2 set of values

  mean1=5; sd1=2; card2 = 250

  lines(min:max,dnorm(min:max,mean1,sd1)*card1,col=2)

  lines(min:max,dnorm(min:max,mean2,sd2)*card2,col=3)

  lines(min:max,dnorm(min:max,mean(c(x1,x2)),sd(c(x1,x2)))*card2,col=4)

 })

dfadd = structure(function# Adding list to a dataframe.

  }

  tf_outputs$lower_bound = tf_outputs$center - tf_outputs$width/2

  tf_outputs$upper_bound = tf_outputs$center + tf_outputs$width/2

  i = 1

  while (i <= length(tf_outputs[,1])) {

    i = i+1

  }

  return(tf_outputs)

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

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) {

		return(clusters)

	}

	strain = samples[[1]]$strain

  min_nuc_center = min(samples[[1]]$roi$begin, samples[[1]]$roi$end)

	max_nuc_center = max(samples[[1]]$roi$begin, samples[[1]]$roi$end)

  # compute clusters

  indexes = c()

  track_readers = c()

  current_nuc = NULL

  # Read nucs from TF outputs

  tf_outs = list()

	i = 1

    new_upper_bound = new_nuc$upper_bound

    if (!is.null(current_nuc)) {

		}

		}

      # aggregate to current cluster

      #   update bound

      if (new_nuc$upper_bound > new_cluster$upper_bound) {

    # store old cluster

    clusters = store_cluster(clusters, new_cluster, nb_nucs_in_cluster,nuc_from_track,length(tf_outs),min_nuc_center, max_nuc_center)

  }

}, ex=function(){

	# Dealing with a region of interest

	roi =list(name="example", begin=1000,  end=1300, chr="1", genome=rep("A",301))

			tmp_nuc_as_list[["nb_reads"]] = length(all_original_reads)

			tmp_nuc_as_list[["nb_nucs"]] = length(tmp_nuc$nucs)

			if (tmp_nuc$wp) {

			} else {

			}

      return(tmp_nuc_as_list)

    })

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.

) {

		print("WARNING, align_inter_strain_nucs will use 2 first sets of replicates as inputs.")

	}

	common_nuc = NULL

	chr = replicates[[1]][[1]]$roi$chr

  min_nuc_center = min(replicates[[1]][[1]]$roi$begin, replicates[[1]][[1]]$roi$end)

	max_nuc_center = max(replicates[[1]][[1]]$roi$begin, replicates[[1]][[1]]$roi$end)

								# tranlation of reads into strain 2 coords

								diff = ((roi_strain_ref1$begin + roi_strain_ref1$end) - (roi_strain_ref2$begin + roi_strain_ref2$end)) / 2

								reads_strain_ref1 = reads_strain_ref1 - rep(diff, length(reads_strain_ref1))

								# Filtering on LOD Score

									tmp_nuc = list()

									# strain_ref1

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

									# tmp_nuc[[paste("corr2_", strain_ref2, sep="")]] = signif(nuc_strain_ref2$nucs[[2]]$corr,5)

									# tmp_nuc[[paste("corr3_", strain_ref2, sep="")]] = signif(nuc_strain_ref2$nucs[[3]]$corr,5)

									# common

									# print(tmp_nuc)

									common_nuc = dfadd(common_nuc, tmp_nuc)

								}

			common_nuc = common_nuc[-to_remove_list,]

		}

	} else {

		print("WARNING, no nucs for strain_ref1.")

		return(NULL)

	}

}, ex=function(){

    # Define new translate_cur function...

        tmp_x_next = tmp_x[-1]

        need_shift = apply(t(tmp_x_next - tmp_x_prev), 2, function(delta){ delta < 50})

        tmp_x_inter = (tmp_x_prev + tmp_x_next) / 2 + tmp_track_inter * need_shift

        new_tmp_x = c()

        new_tmp_y = c()

        index_odd = 1:length(tmp_x) * 2 - 1

        } else {

          pos = config$LEGEND_LOD_POS

        }

      }