/doc/sphinx_doc/build/text/ref.txt - Diff - NucleoMiner - Forge du Centre Blaise Pascal

Révision 6e0010bc doc/sphinx_doc/build/text/ref.txt

     Python Reference
     ================
     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.
     R Reference
     ===========
-...
     Examples
     ~~~~~~~~
            # Define new translate_roi function...
            translate_roi = function(roi, strain2, big_roi=NULL, config=NULL) {
            # Define new translate_cur function...
            translate_cur = function(roi, strain2, big_cur=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"))
            unlockBinding("translate_cur", as.environment("package:nucleominer"))
            unlockBinding("translate_cur", getNamespace("nucleominer"))
            assign("translate_cur", translate_cur, "package:nucleominer")
            assign("translate_cur", translate_cur, getNamespace("nucleominer"))
            lockBinding("translate_cur", getNamespace("nucleominer"))
            lockBinding("translate_cur", 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$strain_ref1)
        roi2 = translate_cur(roi, roi$strain_ref1)
        replicates = list()
        for (j in 1:2) {
            samples = list()
-...
        #       plot_common_nucs = FALSE,
        #       height = 50)
     R: Extract a sub part of the corresponding c2c file
     Extract a sub part of the corresponding c2c file
     ------------------------------------------------
     Description
     ~~~~~~~~~~~
     This fonction allow to acces to a specific part of the c2c file.
     Usage
     ~~~~~
        c2c_extraction(strain1, strain2, chr = NULL, lower_bound = NULL,
            upper_bound = NULL, config = NULL)
     Arguments
     ~~~~~~~~~
     "strain1"
     the key strain
     "strain2"
     the target strain
     "chr"
     if defined, the c2c will filtered according to the chromosome value
     "lower_bound"
     if defined, the c2c will 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
     upper_bound
     "config"
     GLOBAL config variable
     Author(s)
     ~~~~~~~~~
     Florent Chuffart
     R: reformat an "apply manipulated" list of regions
-...
     Usage
     ~~~~~
        compute_inter_all_strain_curs(diff_allowed = 10, min_cur_width = 200,
            config = NULL, plot = FALSE)
        compute_inter_all_strain_curs(diff_allowed = 30, min_cur_width = 4000,
            config = NULL)
     Arguments
-...
     GLOBAL config variable
     "plot"
     Plot CURs or not
     Author(s)
     ~~~~~~~~~
-...
     Description
     ~~~~~~~~~~~
     The fucntion is no more necessary since we remove "big_roi" bug in
     translate_roi function.
     The fucntion is no more necessary since we remove "big_cur" bug in
     translate_cur function.
     Usage
-...
        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
-...
     Usage
     ~~~~~
        flat_aggregated_intra_strain_nucs(partial_strain_maps, roi_index)
        flat_aggregated_intra_strain_nucs(partial_strain_maps, cur_index)
     Arguments
-...
     the output of aggregate_intra_strain_nucs function
     "roi_index"
     "cur_index"
     the index of the roi involved
-...
     Florent Chuffart
     R: Compute the fuzzy nucs.
     R: Compute the fuzzy list for a given strain.
     Compute the fuzzy nucs.
     -----------------------
     Compute the fuzzy list for a given strain.
     ------------------------------------------
     Description
     ~~~~~~~~~~~
     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.
     This function grabs the nucleosomes detxted by template_filter that
     have been rejected bt aggregate_intra_strain_nucs as well positions.
     Usage
     ~~~~~
        get_fuzzy(combi, roi, roi_index, strain_maps, common_nuc_results,
            config = NULL)
        get_intra_strain_fuzzy(wp_map, roi, strain, config = NULL)
     Arguments
     ~~~~~~~~~
     "combi"
     "wp_map"
     The strain combination to consider.
     Well positionned nucleosomes map.
     "roi"
     The region of interest.
     "roi_index"
     The region of interest index.
     "strain_maps"
     Nuc maps.
     "strain"
     "common_nuc_results"
     Common wp nuc maps
     The strain we want to extracvt the fuzzy map.
     "config"
     GLOBAL config variable
     GLOBAL config variable.
     Author(s)
-...
        marker = "H3K4me1"
        combi = c("BY", "YJM")
        form = "wpfuzzy" # "wp" | "fuzzy" | "wpfuzzy"
        form = "wpunr" # "wp" | "unr" | "wpunr"
        # foo = get_sneps(marker, combi, form)
        # foo = get_sneps("H4K12ac", c("BY", "RM"), "wp")
     R: Compute the unaligned nucleosomal regions (UNRs).
     Compute the unaligned nucleosomal regions (UNRs).
     -------------------------------------------------
     Description
     ~~~~~~~~~~~
     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 UNR. It will be take into account in the count read part og
     the pipeline.
     Usage
     ~~~~~
        get_unrs(combi, roi, cur_index, wp_maps, fuzzy_maps, common_nuc_results,
            config = NULL)
     Arguments
     ~~~~~~~~~
     "combi"
     The strain combination to consider.
     "roi"
     The region of interest.
     "cur_index"
     The region of interest index.
     "wp_maps"
     Well positionned nucleosomes maps.
     "fuzzy_maps"
     Fuzzy nucleosomes maps.
     "common_nuc_results"
     Common wp nuc maps
     "config"
     GLOBAL config variable
     Author(s)
     ~~~~~~~~~
     Florent Chuffart
     R: Returns the intersection of 2 list on regions.
     Returns the intersection of 2 list on regions.
     ----------------------------------------------
     Description
     ~~~~~~~~~~~
     This function...
     Usage
     ~~~~~
        intersect_region(region1, region2)
     Arguments
     ~~~~~~~~~
     "region1"
     Original regions.
     "region2"
     Regions to intersect.
     Author(s)
     ~~~~~~~~~
     Florent Chuffart
     R: Likelihood ratio
-...
     +-----------------+-----------------------------------------------------+
     | Author:         | Florent Chuffart                                    |
     +-----------------+-----------------------------------------------------+
     | Version:        | 2.3.29                                              |
     | Version:        | 2.3.40                                              |
     +-----------------+-----------------------------------------------------+
     | License:        | CeCILL                                              |
     +-----------------+-----------------------------------------------------+
-...
     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.
-...
     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: sign from strand
-...
        l = list(key1 = "value1", key2 = "value2")
        print(switch_pairlist(l))
     R: Translate a list of regions from a strain ref to another.
     R: Translate coords of a genome region.
     Translate a list of regions from a strain ref to another.
     ---------------------------------------------------------
     Translate coords of a genome region.
     ------------------------------------
     Description
     ~~~~~~~~~~~
     This function is an eloborated call to translate_roi.
     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_regions(regions, combi, roi_index, config = NULL, roi)
        translate_cur(roi, strain2, config = NULL, big_cur = NULL)
     Arguments
     ~~~~~~~~~
     "regions"
     Regions to be translated.
     "combi"
     "roi"
     Combination of strains.
     Original genome region of interest.
     "roi_index"
     "strain2"
     The region of interest index.
     The strain in wich you want the genome region of interest.
     "config"
     GLOBAL config variable
     "roi"
     "big_cur"
     The region of interest.
     A largest region than roi use to filter c2c if it is needed.
     Author(s)
-...
     Florent Chuffart
     R: Translate coords of a genome region.
     Examples
     ~~~~~~~~
     Translate coords of a genome region.
     ------------------------------------
        # Define new translate_cur function...
        translate_cur = function(roi, strain2, config) {
            strain1 = roi$strain_ref
            if (strain1 == strain2) {
                return(roi)
            } else {
              stop("Here is my new translate_cur function...")
+           }
+       }
        # Binding it by uncomment follwing lines.
        # unlockBinding("translate_cur", as.environment("package:nm"))
        # unlockBinding("translate_cur", getNamespace("nm"))
        # assign("translate_cur", translate_cur, "package:nm")
        # assign("translate_cur", translate_cur, getNamespace("nm"))
        # lockBinding("translate_cur", getNamespace("nm"))
        # lockBinding("translate_cur", as.environment("package:nm"))
     R: Translate a list of regions from a strain ref to another.
     Translate a list of regions from a strain ref to another.
     ---------------------------------------------------------
     Description
     ~~~~~~~~~~~
     This function is used in the examples, usualy you have to define your
     own translation function and overwrite this one using *unlockBinding*
     features. Please, refer to the example.
     This function is an eloborated call to translate_cur.
     Usage
     ~~~~~
        translate_roi(roi, strain2, config = NULL, big_roi = NULL)
        translate_regions(regions, combi, cur_index, config = NULL, roi)
     Arguments
     ~~~~~~~~~
     "roi"
     "regions"
     Original genome region of interest.
     Regions to be translated.
     "strain2"
     "combi"
     The strain in wich you want the genome region of interest.
     Combination of strains.
     "cur_index"
     The region of interest index.
     "config"
     GLOBAL config variable
     "big_roi"
     "roi"
     A largest region than roi use to filter c2c if it is needed.
     The region of interest.
     Author(s)
-...
     Florent Chuffart
     Examples
     ~~~~~~~~
        # Define new translate_roi function...
        translate_roi = function(roi, strain2, config) {
            strain1 = roi$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.
-...
            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)
            change_col = TRUE, plot_wp_nucs = TRUE, plot_fuzzy_nucs = TRUE,
            plot_wp_nuc_model = TRUE, plot_common_nucs = FALSE, plot_common_unrs = FALSE,
            plot_wp_nucs_4_nonmnase = FALSE, plot_chain = FALSE, plot_sample_id = FALSE,
            aggregated_intra_strain_nucs = NULL, aligned_inter_strain_nucs = NULL,
            height = 10, main = NULL, xlab = NULL, ylab = "#reads (per million reads)",
            config = NULL)
     Arguments
-...
     Plot (or not) cluster of nucs
     "plot_fuzzy_nucs"
     Plot (or not) cluster of fuzzy
     "plot_wp_nuc_model"
     Plot (or not) gaussian model for a cluster of nucs
-...
     Plot (or not) aligned reads.
     "plot_anovas"
     Plot (or not) scatter for each nuc.
     "plot_common_unrs"
     "plot_anova_boxes"
     Plot (or not) boxplot for each nuc.
     Plot (or not) unaligned nucleosomal refgions (UNRs).
     "plot_wp_nucs_4_nonmnase"
-...
     Plot (or not) clusterised nuceosomes between mnase samples.
     "plot_sample_id"
     Plot (or not) the sample id for each sample.
     "aggregated_intra_strain_nucs"
     list of aggregated intra strain nucs. If NULL, it will be computed.
-...
     Number of reads in per million read for each sample, graphical
     parametre for the y axis.
     "main"
     main title of the produced plot
     "xlab"
     xlab of the produced plot
     "ylab"
     ylab of the produced plot
     "config"
     GLOBAL config variable

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Révision 6e0010bc doc/sphinx_doc/build/text/ref.txt