LBMC » NucleoMiner

configurator.CSV_SAMPLE_FILE = None

   Path to cvs file that contains sample information.

configurator.BOWTIE_BUILD_BIN = None

   Path for bowtie2 build bin.

configurator.BOWTIE2_BIN = None

   Path for bowtie2 bin.

configurator.SAMTOOLS_BIN = None

   Path for samtools bin.

configurator.BEDTOOLS_BIN = None

   Path for bedtools bin.

configurator.TF_BIN = None

   Path for TemplateFilter bin.

configurator.TF_TEMPLATES_FILE = None

   Path for TemplateFilter templates file.

configurator.ILLUMINA_OUTPUTFILE_PREFIX = None

   Prefix for Illumina fastq output files.

configurator.INDEX_DIR = None

   Path for index dir.

configurator.ALIGN_DIR = None

   Path for align dir.

configurator.LOG_DIR = None

   Path for log dir

configurator.CACHE_DIR = None

   Path for cache dir.

configurator.RESULTS_DIR = None

   Path for results dir

configurator.FASTA_REFERENCE_GENOME_FILES = None

   Dictionary where each fasta reference genomes is indexed by

   reference strain that it corresponds.

configurator.AREA_BLACK_LIST = None

   Dictionary where keys are strain and values are black listed of

   geneome region.

configurator.FASTA_INDEXES = None

   Dictionary of strain that indexes dictionaries where keys are

   chromosome reference from Fastq file and value are its

   correspondance for Templatefilter.

configurator.C2C_FILES = None

   Dictionary where each strain combination indexes genome aligment.

configurator.READ_LENGTH = None

   Length of Illumina reads.

configurator.MAPQ_THRES = None

   Aligment quality thresold.

configurator.TF_CORR = None

   TemplateFilter Template correlation threshold.

configurator.TF_MINW = None

   TemplateFilter minimum width of a nucleosome.

configurator.TF_MAXW = None

   TemplateFilter maximum  width of a nucleosome.

configurator.TF_OL = None

   TemplateFilter maximum allowed overlap for two nucleosomes.

libcoverage.create_bowtie_index(strain, strain_fasta_ref, index_dir, bowtie_build_bin)

   Creates bowtie index for a strain *strain*.

   Parameters:

      * **strain** -- the strain reference.

      * **strain_fasta_ref** -- fasta reference genome.

      * **index_dir** -- directories where to put bowtie index.

      * **bowtie_build_bin** -- bowtie2 build binary.

libcoverage.align_reads(sample, align_dir, log_dir, index_dir, illumina_outputfile_prefix, bowtie2_bin, samtools_bin, bedtools_bin)

   Aligns reads to reference genomes. It produces .sam files, that are

   converted to .bam, that are converted to .bed.

   Parameters:

      * **sample** -- a dict that describe a sample.

      * **align_dir** -- directory where aligned reads will be

        stored.

      * **log_dir** -- directory where logs will be stored.

      * **illumina_outputfile_prefix** -- prefix of Illumina

        sequencer fastq.gz output files.

      * **bowtie2_bin** -- bowtie2 binary.

      * **samtools_bin** -- samtools binary.

      * **bedtools_bin** -- bedtools binary.

      * **index_dir** -- bowtie index directory.

libcoverage.split_fr_4_TF(sample, align_dir, fasta_indexes, area_black_list, read_length, mapq_thres)

   Create TempleFilter input files form bed files. This function

   appends in two times. First, it collects reads from bed files and

   feeds a datastructure

   Parameters:

      * **sample** -- a dict that describe a sample.

      * **align_dir** -- directory where aligned reads will be

        stored.

      * **fasta_index** -- the chr reference from the illumina

        output file.

      * **area_black_list** -- the description of genome that will

        be omit.

      * **read_length** -- Length of Illumina reads.

      * **mapq_thres** -- mapping quality criterion threshold, see

        MAPQ in BED/BAM file format.

libcoverage.template_filter(sample, align_dir, log_dir, tf_bin, tf_templates_file, corr, minw, maxw, ol)

   Run TemplateFilter on a specifi sample. It produces .tab file.

   Parameters:

      * **sample** -- a dict that describe a sample.

      * **align_dir** -- directory where aligned reads will be

        stored.

      * **log_dir** -- directory where logs will be stored.

      * **tf_bin** -- path to the TemplateFilter binary.

      * **tf_templates_file** -- path to the TemplateFilter

        templates file.

      * **corr** -- correlation threshold transmits to

        TemplateFilter.

      * **minw** -- minimum width of a nuc, transmits to

        TemplateFilter.

      * **maxw** -- maximum width of a nuc, transmits to

        TemplateFilter.

      * **ol** -- maximum overlaps for 2 nuc, transmits to

        TemplateFilter.

       # Define new translate_roi function...

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

       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"))

   roi2 = translate_roi(roi, roi$strain_ref1)

   compute_inter_all_strain_curs(diff_allowed = 10, min_cur_width = 200,

       config = NULL, plot = FALSE)

"plot"

Plot CURs or not

The fucntion is no more necessary since we remove "big_roi" bug in

translate_roi function.

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

   flat_aggregated_intra_strain_nucs(partial_strain_maps, roi_index)

"roi_index"

R: Compute the fuzzy nucs.

Compute the fuzzy nucs.

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

This function aggregate non common wp nucs for each strain and

substract common wp nucs. It does not take care about the size of the

resulting fuzzy regions. It will be take into account in the count

read part og the pipeline.

   get_fuzzy(combi, roi, roi_index, strain_maps, common_nuc_results,

       config = NULL)

"combi"

The strain combination to consider.

"roi_index"

The region of interest index.

"strain_maps"

Nuc maps.

"common_nuc_results"

Common wp nuc maps

GLOBAL config variable

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

| Version:        | 2.3.29                                              |

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: Remove wp nucs from common nucs list.

Remove wp nucs from common nucs list.

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

Description

~~~~~~~~~~~

It is based on common wp nucs index on nucs and region.

Usage

~~~~~

   remove_aligned_wp(strain_maps, roi_index, tmp_common_nucs, strain)

Arguments

~~~~~~~~~

"strain_maps"

Nuc maps.

"roi_index"

The region of interest index.

"tmp_common_nucs"

the list of wp nucs.

"strain"

The strain to consider.

Author(s)

~~~~~~~~~

Florent Chuffart

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

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

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

This function is an eloborated call to translate_roi.

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

"regions"

Regions to be translated.

"combi"

Combination of strains.

"roi_index"

The region of interest index.

"roi"

The region of interest.

R: Translate coords of a genome region.

Translate coords of a genome region.

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

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.

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

"roi"

Original genome region of interest.

"strain2"

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

"big_roi"

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

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"))

       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)

"plot_anovas"

Plot (or not) scatter for each nuc.

"plot_anova_boxes"

Plot (or not) boxplot for each nuc.

configurator.CSV_SAMPLE_FILE = None

   Path to cvs file that contains sample information.

configurator.ILLUMINA_OUTPUTFILE_PREFIX = None

   Prefix for Illumina fastq output files.

configurator.FASTA_REFERENCE_GENOME_FILES = None

   Dictionary where each fasta reference genomes is indexed by

   reference strain that it corresponds.

configurator.FASTA_INDEXES = None

   Dictionary of strain that indexes dictionaries where keys are

   chromosome reference from Fastq file and value are its

   correspondance for Templatefilter.

configurator.AREA_BLACK_LIST = None

   Dictionary where keys are strain and values are black listed of

   geneome region.

configurator.C2C_FILES = None

   Dictionary where each strain combination indexes genome aligment.

version = '2.3.39'

release = '2.3.39'

| Version:      | 2.3.39                                            |

        plot_wp_nucs_4_nonmnase = FALSE, plot_chain = FALSE, aggregated_intra_strain_nucs = NULL, 

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

Version: 2.3.39

  plot(c(x_min_glo,x_max_glo), c(0,0), ylim=ylim_glo, col=0, yaxt="n", ylab="#reads (per million reads)", xlab=paste("Ref strain:", replicates[[1]][[1]]$strain, "chr: ", replicates[[1]][[1]]$roi$chr), main="NucleoMiner2" )

			text(x_min_glo, y_lev + height/2 - delta_y_glo/100, labels=paste("(",sample$id,") ",sample$strain, " ", sample$marker, sep=""))

            }

							lines(sign(x_min) * delta_x + shift, dnorm(delta_x, mean(flatted_reads[[3]]), sd(flatted_reads[[3]])) * length(flatted_reads[[3]]) * height/5 + y_lev, col=col, lty=2)

        tmp_track_inter = signif(tmp_track_prev - tmp_track_next) * (abs(tmp_track_prev - tmp_track_next) > 1) * 25

        text(tmp_x_inter, tmp_y_inter, tmp_lod_inter, srt=90, cex=0.9, bg = "yellow")#, col=(tmp_lod_inter < 20) + 2)

      rect(sign(x_min[[1]]) * unrs$lower_bound + shift[[1]], y_min[[1]], sign(x_min[[1]]) * unrs$upper_bound + shift[[1]], y_max[[2]], col=adjustcolor(4, alpha.f = 0.3), border=1)