LBMC » NucleoMiner

Arabic to Roman pair list.

--------------------------

Description

~~~~~~~~~~~

Util to convert Arabicto Roman

Usage

~~~~~

::

    ARAB2ROM()

Author(s)

~~~~~~~~~

Florent Chuffart

R: False Discovery Rate

False Discovery Rate

--------------------

Description

~~~~~~~~~~~

From a vector x of independent p-values, extract the cutoff

corresponding to the specified FDR. See Benjamini & Hochberg 1995 paper

Usage

~~~~~

::

    FDR(x, FDR)

Arguments

~~~~~~~~~

``x``

A vector x of independent p-values.

``FDR``

The specified FDR.

Value

~~~~~

Return the the corresponding cutoff.

Author(s)

~~~~~~~~~

Gael Yvert, Florent Chuffart

Examples

~~~~~~~~

::

    print("example")

R: Roman to Arabic pair list.

Roman to Arabic pair list.

--------------------------

Description

~~~~~~~~~~~

Util to convert Roman to Arabic

Usage

~~~~~

::

    ROM2ARAB()

Author(s)

~~~~~~~~~

Florent Chuffart

R: Aggregate replicated sample's nucleosomes.

Aggregate replicated sample's nucleosomes.

------------------------------------------

Description

~~~~~~~~~~~

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 *lod\_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.

Usage

~~~~~

::

    aggregate_intra_strain_nucs(samples, lod_thres = 20, coord_max = 2e+07)

Arguments

~~~~~~~~~

``samples``

A list of samples. Each sample is a list like *sample = list(id=...,

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

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

``lod_thres``

Log likelihood ration threshold.

``coord_max``

A too big value to be a coord for a nucleosome lower bound.

Value

~~~~~

Returns a list of clusterized nucleosomes, and all computed lod scores.

Author(s)

~~~~~~~~~

Florent Chuffart

Examples

~~~~~~~~

::

    # Dealing with a region of interest

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

    samples = list()

    for (i in 1:3) {

        # Create TF output

        tf_nuc = list("chr"=paste("chr", roi$chr, sep=""), "center"=(roi$end + roi$begin)/2, "width"= 150, "correlation.score"= 0.9)

        outputs = dfadd(NULL,tf_nuc)

        outputs = filter_tf_outputs(outputs, roi$chr, roi$begin, roi$end)

        # Generate corresponding reads

        nb_reads = round(runif(1,170,230))

        reads = round(rnorm(nb_reads, tf_nuc$center,20))

        u_reads = sort(unique(reads))

        strands = sample(c(rep("R",ceiling(length(u_reads)/2)),rep("F",floor(length(u_reads)/2))))

        counts = apply(t(u_reads), 2, function(r) { sum(reads == r)})

        shifts = apply(t(strands), 2, function(s) { if (s == "F") return(-tf_nuc$width/2) else return(tf_nuc$width/2)})

        u_reads = u_reads + shifts

        inputs = data.frame(list("V1" = rep(roi$chr, length(u_reads)),

                                 "V2" = u_reads,

                                                         "V3" = strands,

                                                         "V4" = counts), stringsAsFactors=FALSE)

        samples[[length(samples) + 1]] = list(id=1, marker="Mnase_Seq", strain="strain_ex", total_reads = 10000000, roi=roi, inputs=inputs, outputs=outputs)

    }

    print(aggregate_intra_strain_nucs(samples))

R: Aligns nucleosomes between 2 strains.

Aligns nucleosomes between 2 strains.

-------------------------------------

Description

~~~~~~~~~~~

This function aligns nucs between two strains for a given genome region.

Usage

~~~~~

::

    align_inter_strain_nucs(replicates, wp_nucs_strain_ref1 = NULL, 

        wp_nucs_strain_ref2 = NULL, corr_thres = 0.5, lod_thres = 100, 

        config = NULL, ...)

Arguments

~~~~~~~~~

``replicates``

Set of replicates, ideally 3 per strain.

``wp_nucs_strain_ref1``

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

be computed.

``corr_thres``

Correlation threshold.

``lod_thres``

LOD cut off.

``config``

GLOBAL config variable

``...``

A list of parameters that will be passed to

*aggregate\_intra\_strain\_nucs* if needed.

Value

~~~~~

Returns a list of clusterized nucleosomes, and all computed lod scores.

Author(s)

~~~~~~~~~

Florent Chuffart

Examples

~~~~~~~~

::

        # Define new translate_roi function...

        translate_roi = function(roi, strain2, big_roi=NULL, config=NULL) {

          return(roi)

        }

        # Binding it by uncomment follwing lines.

        unlockBinding("translate_roi", as.environment("package:nucleominer"))

        unlockBinding("translate_roi", getNamespace("nucleominer"))

        assign("translate_roi", translate_roi, "package:nucleominer")

        assign("translate_roi", translate_roi, getNamespace("nucleominer"))

        lockBinding("translate_roi", getNamespace("nucleominer"))

        lockBinding("translate_roi", as.environment("package:nucleominer"))

    # Dealing with a region of interest

    roi =list(name="example", begin=1000,  end=1300, chr="1", genome=rep("A",301), strain_ref1 = "STRAINREF1")

    roi2 = translate_roi(roi, roi$strain_ref1)

    replicates = list()

    for (j in 1:2) {

        samples = list()

        for (i in 1:3) {

            # Create TF output

            tf_nuc = list("chr"=paste("chr", roi$chr, sep=""), "center"=(roi$end + roi$begin)/2, "width"= 150, "correlation.score"= 0.9)

            outputs = dfadd(NULL,tf_nuc)

            outputs = filter_tf_outputs(outputs, roi$chr, roi$begin, roi$end)

            # Generate corresponding reads

            nb_reads = round(runif(1,170,230))

            reads = round(rnorm(nb_reads, tf_nuc$center,20))

            u_reads = sort(unique(reads))

            strands = sample(c(rep("R",ceiling(length(u_reads)/2)),rep("F",floor(length(u_reads)/2))))

            counts = apply(t(u_reads), 2, function(r) { sum(reads == r)})

            shifts = apply(t(strands), 2, function(s) { if (s == "F") return(-tf_nuc$width/2) else return(tf_nuc$width/2)})

            u_reads = u_reads + shifts

            inputs = data.frame(list("V1" = rep(roi$chr, length(u_reads)),

                                     "V2" = u_reads,

                                                             "V3" = strands,

                                                             "V4" = counts), stringsAsFactors=FALSE)

            samples[[length(samples) + 1]] = list(id=1, marker="Mnase_Seq", strain=paste("strain_ex",j,sep=""), total_reads = 10000000, roi=roi, inputs=inputs, outputs=outputs)

        }

        replicates[[length(replicates) + 1]] = samples

    }

    print(align_inter_strain_nucs(replicates))

R: 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.

Usage

~~~~~

::

    analyse_design(snep_design, reads)

Arguments

~~~~~~~~~

``snep_design``

The design to considere.

``reads``

The data to considere.

Author(s)

~~~~~~~~~

Florent Chuffart

R: Stage replicates data

Stage replicates data

---------------------

Description

~~~~~~~~~~~

This function loads in memory data corresponding to the given

experiments.

Usage

~~~~~

::

    build_replicates(expe, roi, only_fetch = FALSE, get_genome = FALSE, 

        all_samples, config = NULL)

Arguments

~~~~~~~~~

``expe``

a list of vector corresponding to vector of replicates.

``roi``

the region that we are interested in.

``only_fetch``

filter or not inputs.

``get_genome``

Load or not corresponding genome.

``all_samples``

Global list of samples.

``config``

GLOBAL config variable.

Author(s)

~~~~~~~~~

Florent Chuffart

Examples

~~~~~~~~

::

    # library(rjson)

    # library(nucleominer)

    #

    # # Read config file

    # json_conf_file = "nucleo_miner_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)

    # # here are the sample ids in a list

    # expes = list(c(1))

    # # here is the region that we wnt to see the coverage

    # cur = list(chr="8", begin=472000, end=474000, strain_ref="BY")

    # # it displays the corverage

    # replicates = build_replicates(expes, cur, all_samples=all_samples, config=config)

    # out = watch_samples(replicates, config$READ_LENGTH,

    #       plot_coverage = TRUE,

    #       plot_squared_reads = FALSE,

    #       plot_ref_genome = FALSE,

    #       plot_arrow_raw_reads = FALSE,

    #       plot_arrow_nuc_reads = FALSE,

    #       plot_gaussian_reads = FALSE,

    #       plot_gaussian_unified_reads = FALSE,

    #       plot_ellipse_nucs = FALSE,

    #       plot_wp_nucs = FALSE,

    #       plot_wp_nuc_model = FALSE,

    #       plot_common_nucs = FALSE,

    #       height = 50)

R: reformat an "apply manipulated" list of regions

reformat an "apply manipulated" list of regions

-----------------------------------------------

Description

~~~~~~~~~~~

Utils to reformat an "apply manipulated" list of regions

Usage

~~~~~

::

    collapse_regions(regions)

Arguments

~~~~~~~~~

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

| ``regions``   |    |

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

Author(s)

~~~~~~~~~

Florent Chuffart

R: Compute Common Uninterrupted Regions (CUR)

Compute Common Uninterrupted Regions (CUR)

------------------------------------------

Description

~~~~~~~~~~~

CURs are regions that can be aligned between the genomes

Usage

~~~~~

::

    compute_inter_all_strain_curs(diff_allowed = 10, min_cur_width = 200, 

        config = NULL, plot = FALSE)

Arguments

~~~~~~~~~

``diff_allowed``

the maximum indel width allowe din a CUR

``min_cur_width``

The minimum width of a CUR

``config``

GLOBAL config variable

``plot``

Plot CURs or not

Author(s)

~~~~~~~~~

Florent Chuffart

R: Crop bound of regions according to region of interest bound

Crop bound of regions according to region of interest bound

-----------------------------------------------------------

Description

~~~~~~~~~~~

The fucntion is no more necessary since we remove "big\_roi" bug in

translate\_roi function.

Usage

~~~~~

::

    crop_fuzzy(tmp_fuzzy_nucs, roi, strain, config = NULL)

Arguments

~~~~~~~~~

``tmp_fuzzy_nucs``

the regiuons to be croped.

``roi``

The region of interest.

``strain``

The strain to consider.

``config``

GLOBAL config variable

Author(s)

~~~~~~~~~

Florent Chuffart

R: Adding list to a dataframe.

Adding list to a dataframe.

---------------------------

Description

~~~~~~~~~~~

Add a list *l* to a dataframe *df*. Create it if *df* is *NULL*. Return

the dataframe *df*.

Usage

~~~~~

::

    dfadd(df, l)

Arguments

~~~~~~~~~

``df``

A dataframe

``l``

A list

Value

~~~~~

Return the dataframe *df*.

Author(s)

~~~~~~~~~

Florent Chuffart

Examples

~~~~~~~~

::

    ## Here dataframe is NULL

    print(df)

    df = NULL

    # Initialize df

    df = dfadd(df, list(key1 = "value1", key2 = "value2"))

    print(df)

    # Adding elements to df

    df = dfadd(df, list(key1 = "value1'", key2 = "value2'"))

    print(df)

R: Extract wp nucs from nuc map.

Extract wp nucs from nuc map.

-----------------------------

Description

~~~~~~~~~~~

Function based on common wp nuc index and roi\_index.

Usage

~~~~~

::

    extract_wp(strain_maps, roi_index, strain, tmp_common_nucs)

Arguments

~~~~~~~~~

``strain_maps``

Nuc maps.

``roi_index``

The region of interest index.

``strain``

The strain to consider.

``tmp_common_nucs``

the list of wp nucs.

Author(s)

~~~~~~~~~

Florent Chuffart

R: Prefetch data

Prefetch data

-------------

Description

~~~~~~~~~~~

Fetch and filter inputs and outpouts per region of interest. Organize it

per replicates.

Usage

~~~~~

::

    fetch_mnase_replicates(strain, roi, all_samples, config = NULL, 

        only_fetch = FALSE, get_genome = FALSE, get_ouputs = TRUE)

Arguments

~~~~~~~~~

``strain``

The strain we want mnase replicatesList of replicates. Each replicates

is a vector of sample ids.

``roi``

Region of interest.

``all_samples``

Global list of samples.

``config``

GLOBAL config variable

``only_fetch``

If TRUE, only fetch and not filtering. It is used tio load sample files

into memory before forking.

``get_genome``

If TRUE, load corresponding genome sequence.

``get_ouputs``

If TRUE, get also ouput corresponding TF output files.

Author(s)

~~~~~~~~~

Florent Chuffart

R: Filter TemplateFilter inputs

Filter TemplateFilter inputs

----------------------------

Description

~~~~~~~~~~~

This function filters TemplateFilter inputs according genome area

observed properties. It takes into account reads that are at the

frontier of this area and the strand of these reads.

Usage

~~~~~

::

    filter_tf_inputs(inputs, chr, x_min, x_max, nuc_width = 160, 

        only_f = FALSE, only_r = FALSE, filter_for_coverage = FALSE)

Arguments

~~~~~~~~~

``inputs``

TF inputs to be filtered.

``chr``

Chromosome observed, here chr is an integer.

``x_min``

Coordinate of the first bp observed.

``x_max``

Coordinate of the last bp observed.

``nuc_width``

Nucleosome width.

``only_f``

Filter only F reads.

``only_r``

Filter only R reads.

``filter_for_coverage``

Does it filter for plot coverage?

Value

~~~~~

Returns filtred inputs.

Author(s)

~~~~~~~~~

Florent Chuffart

R: Filter TemplateFilter outputs

Filter TemplateFilter outputs

-----------------------------

Description

~~~~~~~~~~~

This function filters TemplateFilter outputs according, not only genome

area observerved properties, but also correlation and overlap threshold.

Usage

~~~~~

::

    filter_tf_outputs(tf_outputs, chr, x_min, x_max, nuc_width = 160, 

        ol_bp = 59, corr_thres = 0.5)

Arguments

~~~~~~~~~

``tf_outputs``

TemplateFilter outputs.

``chr``

Chromosome observed, here chr is an integer.

``x_min``

Coordinate of the first bp observed.

``x_max``

Coordinate of the last bp observed.

``nuc_width``

Nucleosome width.

``ol_bp``

Overlap Threshold.

``corr_thres``

Correlation threshold.

Value

~~~~~

Returns filtered TemplateFilter Outputs

Author(s)

~~~~~~~~~

Florent Chuffart

R: to flat aggregate\_intra\_strain\_nucs function output

to flat aggregate\_intra\_strain\_nucs function output

------------------------------------------------------

Description

~~~~~~~~~~~

This function builds a dataframe of all clusters obtain from

aggregate\_intra\_strain\_nucs function.

Usage

~~~~~

::

    flat_aggregated_intra_strain_nucs(partial_strain_maps, roi_index)

Arguments

~~~~~~~~~

``partial_strain_maps``

the output of aggregate\_intra\_strain\_nucs function

``roi_index``

the index of the roi involved

Value

~~~~~

Returns a dataframe of all clusters obtain from

aggregate\_intra\_strain\_nucs function.

Author(s)

~~~~~~~~~

Florent Chuffart

R: flat reads

flat reads

----------

Description

~~~~~~~~~~~

Extract reads coordinates from TempleteFilter input sequence

Usage

~~~~~

::

    flat_reads(reads, nuc_width)

Arguments

~~~~~~~~~

``reads``

TemplateFilter input reads

``nuc_width``

Width used to shift F and R reads.

Value

~~~~~

Returns a list of F reads, R reads and joint/shifted F and R reads.

Author(s)

~~~~~~~~~

Florent Chuffart

R: Retrieve Reads

Retrieve Reads

--------------

Description

~~~~~~~~~~~

Retrieve reads for a given marker, combi, form.

Usage

~~~~~

::

    get_all_reads(marker, combi, form = "wp", config = NULL)

Arguments

~~~~~~~~~

``marker``

The marker to considere.

``combi``

The starin combination to considere.

``form``

The nuc form to considere.

``config``

GLOBAL config variable

Author(s)

~~~~~~~~~

Florent Chuffart

R: get comp strand

get comp strand

---------------

Description

~~~~~~~~~~~

Compute the complementatry strand.

Usage

~~~~~

::

    get_comp_strand(strand)

Arguments

~~~~~~~~~

``strand``

The original strand.

Value

~~~~~

Returns the complementatry strand.

Author(s)

~~~~~~~~~

Florent Chuffart

R: Build the design for deseq

Build the design for deseq

--------------------------

Description

~~~~~~~~~~~

This function build the design according sample properties.

Usage

~~~~~

::

    get_design(marker, combi, all_samples)

Arguments

~~~~~~~~~

``marker``

The marker to considere.

``combi``

The starin combination to considere.

``all_samples``

Global list of samples.

Author(s)

~~~~~~~~~

Florent Chuffart

R: Compute the list of SNEPs for a given set of marker, strain...

Compute the list of SNEPs for a given set of marker, strain combination and nuc form.

-------------------------------------------------------------------------------------

Description

~~~~~~~~~~~

This function uses

Usage

~~~~~

::

    get_sneps(marker, combi, form, all_samples, config = NULL)

Arguments

~~~~~~~~~

``marker``

The marker involved.

``combi``

The strain combination involved.

``form``

the nuc form involved.

``all_samples``

Global list of samples.

``config``

GLOBAL config variable

Author(s)

~~~~~~~~~

Florent Chuffart

Examples

~~~~~~~~

::

    marker = "H3K4me1"

    combi = c("BY", "YJM")

    form = "wpfuzzy" # "wp" | "fuzzy" | "wpfuzzy"

    # foo = get_sneps(marker, combi, form)

    # foo = get_sneps("H4K12ac", c("BY", "RM"), "wp")

R: Likelihood ratio

Likelihood ratio

----------------

Description

~~~~~~~~~~~

Compute the likelihood log of two set of value from two models Vs. a

unique model.

Usage

~~~~~

::

    lod_score_vecs(x, y)

Arguments

~~~~~~~~~

``x``

First vector.

``y``

Second vector.

Value

~~~~~

Returns the likelihood ratio.

Author(s)

~~~~~~~~~

Florent Chuffart

Examples

~~~~~~~~

::

    # LOD score for 2 set of values

    mean1=5; sd1=2; card2 = 250

    mean2=6; sd2=3; card1 = 200

    x1 = rnorm(card1, mean1, sd1)

    x2 = rnorm(card2, mean2, sd2)

    min = floor(min(c(x1,x2)))

    max = ceiling(max(c(x1,x2)))

    hist(c(x1,x2), xlim=c(min, max), breaks=min:max)

    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)

    lod_score_vecs(x1,x2)

R: nm

nm

--

Description

~~~~~~~~~~~

It provides a set of useful functions allowing to perform quantitative

analysis of nucleosomal epigenome.

Details

~~~~~~~

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

| Package:      | nucleominer                                       |

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

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

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

| Author:       | Florent Chuffart                                  |

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

| Version:      | 2.3.31                                            |

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

| License:      | CeCILL                                            |

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

| Title:        | nm                                                |

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

| Depends:      | seqinr, plotrix, DESeq, cachecache                |

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

Author(s)

~~~~~~~~~

Florent Chuffart

R: Performaing ANOVAs

Performaing ANOVAs

------------------

Description

~~~~~~~~~~~

Counts reads and Performs ANOVAS for each common nucleosomes involved.

Usage

~~~~~

::

    perform_anovas(replicates, aligned_inter_strain_nucs, inputs_name = "Mnase_Seq", 

        plot_anova_boxes = FALSE)

Arguments

~~~~~~~~~

``replicates``

Set of replicates, each replicate is a list of samples (ideally 3). Each

sample is a list like *sample = list(id=..., marker=..., strain=...,

roi=..., inputs=..., outputs=...)* with *roi = list(name=..., begin=...,

end=..., chr=..., genome=...)*. In the *perform\_anovas* contexte, we

need 4 replicates (4 \* (3 samples)): 2 strains \* (1 marker + 1 input

(Mnase\_Seq)).

``aligned_inter_strain_nucs``

List of common nucleosomes.

``inputs_name``

Name of the input.

``plot_anova_boxes``

Plot (or not) boxplot for each nuc.

Value

~~~~~

Returns ANOVA results and comunted reads.

Author(s)

~~~~~~~~~

Florent Chuffart

R: Plot the distribution of reads.

Plot the distribution of reads.

-------------------------------

Description

~~~~~~~~~~~

This fuxntion use the deseq nomalization feature to compare

qualitatively the distribution.

Usage

~~~~~

::

    plot_dist_samples(strain, marker, res, all_samples, NEWPLOT = TRUE)

Arguments

~~~~~~~~~

``strain``

The strain to considere.

``marker``

The marker to considere.

``res``

Data

``all_samples``

Global list of samples.

``NEWPLOT``

If FALSE the curve will be add to the current plot.

Author(s)

~~~~~~~~~

Florent Chuffart

R: sign from strand

sign from strand

----------------

Description

~~~~~~~~~~~

Get the sign of strand

Usage

~~~~~

::

    sign_from_strand(strands)

Arguments

~~~~~~~~~

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

| ``strands``   |    |

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

Value

~~~~~

If strand in forward then returns 1 else returns -1

Author(s)

~~~~~~~~~

Florent Chuffart

R: Substract to a list of regions an other list of regions that...

Substract to a list of regions an other list of regions that intersect it.

--------------------------------------------------------------------------

Description

~~~~~~~~~~~

This fucntion embed a recursive part. It occurs when a substracted

region split an original region on two.

Usage

~~~~~

::

    substract_region(region1, region2)

Arguments

~~~~~~~~~

``region1``

Original regions.

``region2``

Regions to substract.

Author(s)

~~~~~~~~~

Florent Chuffart

R: Switch a pairlist

Switch a pairlist

-----------------

Description

~~~~~~~~~~~

Take a pairlist key:value and return the switched pairlist value:key.

Usage

~~~~~

::

    switch_pairlist(l)

Arguments

~~~~~~~~~

``l``

The pairlist to switch.

Value

~~~~~

The switched pairlist.

Author(s)

~~~~~~~~~

Florent Chuffart

Examples

~~~~~~~~

::

    l = list(key1 = "value1", key2 = "value2")

    print(switch_pairlist(l))

R: Translate a list of regions from a strain ref to another.

Translate a list of regions from a strain ref to another.

---------------------------------------------------------

Description

~~~~~~~~~~~

This function is an eloborated call to translate\_roi.

Usage

~~~~~

::

    translate_regions(regions, combi, roi_index, config = NULL, roi)

Arguments

~~~~~~~~~

``regions``

Regions to be translated.

``combi``

Combination of strains.

``roi_index``

The region of interest index.

``config``

GLOBAL config variable

``roi``

The region of interest.

Author(s)

~~~~~~~~~

Florent Chuffart

R: Translate coords of a genome region.

Translate coords of a genome region.

------------------------------------

Description

~~~~~~~~~~~

This function is used in the examples, usualy you have to define your

own translation function and overwrite this one using *unlockBinding*

features. Please, refer to the example.

Usage

~~~~~

::

    translate_roi(roi, strain2, config = NULL, big_roi = NULL)

Arguments

~~~~~~~~~

``roi``

Original genome region of interest.

``strain2``

The strain in wich you want the genome region of interest.

``config``

GLOBAL config variable

``big_roi``

A largest region than roi use to filter c2c if it is needed.

Author(s)

~~~~~~~~~

Florent Chuffart

Examples

~~~~~~~~

::

    # Define new translate_roi function...

    translate_roi = function(roi, strain2, config) {

        strain1 = roi$strain_ref

        if (strain1 == strain2) {

            return(roi)

        } else {

          stop("Here is my new translate_roi function...")      

        }   

    }

    # Binding it by uncomment follwing lines.

    # unlockBinding("translate_roi", as.environment("package:nm"))

    # unlockBinding("translate_roi", getNamespace("nm"))

    # assign("translate_roi", translate_roi, "package:nm")

    # assign("translate_roi", translate_roi, getNamespace("nm"))

    # lockBinding("translate_roi", getNamespace("nm"))

    # lockBinding("translate_roi", as.environment("package:nm"))    

R: Aggregate regions that intersect themnselves.

Aggregate regions that intersect themnselves.

---------------------------------------------

Description

~~~~~~~~~~~

This function is based on sort of lower bounds to detect regions that

intersect. We compare lower bound and upper bound of the porevious item.

This function embed a while loop and break break regions list become

stable.

Usage

~~~~~

::

    union_regions(regions)

Arguments

~~~~~~~~~

``regions``

The Regions to be aggregated

Author(s)

~~~~~~~~~

Florent Chuffart

R: Watching analysis of samples

Watching analysis of samples

----------------------------

Description

~~~~~~~~~~~

This function allows to view analysis for a particuler region of the

genome.

Usage

~~~~~

::

    watch_samples(replicates, read_length, plot_ref_genome = TRUE, 

        plot_arrow_raw_reads = TRUE, plot_arrow_nuc_reads = TRUE, 

        plot_squared_reads = TRUE, plot_coverage = FALSE, plot_gaussian_reads = TRUE, 

        plot_gaussian_unified_reads = TRUE, plot_ellipse_nucs = TRUE, 

        change_col = 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, plot_chain = FALSE, aggregated_intra_strain_nucs = NULL, 

        aligned_inter_strain_nucs = NULL, height = 10, config = NULL)

Arguments

~~~~~~~~~

``replicates``

replicates under the form...

``read_length``

length of the reads

``plot_ref_genome``

Plot (or not) reference genome.

``plot_arrow_raw_reads``

Plot (or not) arrows for raw reads.

``plot_arrow_nuc_reads``

Plot (or not) arrows for reads aasiocied to a nucleosome.

``plot_squared_reads``

Plot (or not) reads in the square fashion.

``plot_coverage``

Plot (or not) reads in the covergae fashion. fashion.

``plot_gaussian_reads``

Plot (or not) gaussian model of a F anf R reads.

``plot_gaussian_unified_reads``

Plot (or not) gaussian model of a nuc.

``plot_ellipse_nucs``

Plot (or not) ellipse for a nuc.

``change_col``

Change the color of each nucleosome.

``plot_wp_nucs``

Plot (or not) cluster of nucs

``plot_wp_nuc_model``

Plot (or not) gaussian model for a cluster of nucs

``plot_common_nucs``

Plot (or not) aligned reads.

``plot_anovas``

Plot (or not) scatter for each nuc.

``plot_anova_boxes``

Plot (or not) boxplot for each nuc.

``plot_wp_nucs_4_nonmnase``

Plot (or not) clusters for non inputs samples.

``plot_chain``

Plot (or not) clusterised nuceosomes between mnase samples.

``aggregated_intra_strain_nucs``

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

``aligned_inter_strain_nucs``

list of aligned inter strain nucs. If NULL, it will be computed.

``height``