Révision 9fdbfada doc/sphinx_doc/rref.rst
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Florent Chuffart |
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R: Compute the fuzzy list for a given strain. |
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Compute the fuzzy list for a given strain. |
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------------------------------------------ |
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Description |
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~~~~~~~~~~~ |
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This function grabs the nucleosomes detxted by template\_filter that |
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have been rejected bt aggregate\_intra\_strain\_nucs as well positions. |
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Usage |
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~~~~~ |
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:: |
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get_intra_strain_fuzzy(wp_maps, roi, strain, config = NULL) |
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Arguments |
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~~~~~~~~~ |
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``wp_maps`` |
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Well positionned nucleosomes map. |
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``roi`` |
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The region of interest. |
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``strain`` |
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The strain we want to extracvt the fuzzy map. |
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``config`` |
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GLOBAL config variable. |
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Author(s) |
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~~~~~~~~~ |
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Florent Chuffart |
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R: Compute the list of SNEPs for a given set of marker, strain... |
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Compute the list of SNEPs for a given set of marker, strain combination and nuc form. |
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# foo = get_sneps(marker, combi, form) |
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# foo = get_sneps("H4K12ac", c("BY", "RM"), "wp")
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R: Compute the unaligned nucleosomal regions (UNRs). |
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Compute the unaligned nucleosomal regions (UNRs). |
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------------------------------------------------- |
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Description |
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~~~~~~~~~~~ |
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This function aggregate non common wp nucs for each strain and substract |
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common wp nucs. It does not take care about the size of the resulting |
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UNR. It will be take into account in the count read part og the |
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pipeline. |
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Usage |
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~~~~~ |
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:: |
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get_unrs(combi, roi, roi_index, wp_maps, fuzzy_maps, common_nuc_results, |
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config = NULL) |
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Arguments |
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~~~~~~~~~ |
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``combi`` |
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The strain combination to consider. |
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``roi`` |
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The region of interest. |
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``roi_index`` |
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The region of interest index. |
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``wp_maps`` |
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Well positionned nucleosomes maps. |
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``fuzzy_maps`` |
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Fuzzy nucleosomes maps. |
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``common_nuc_results`` |
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Common wp nuc maps |
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``config`` |
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GLOBAL config variable |
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Author(s) |
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~~~~~~~~~ |
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Florent Chuffart |
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R: Returns the intersection of 2 list on regions. |
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Returns the intersection of 2 list on regions. |
| ... | ... | |
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+---------------+---------------------------------------------------+ |
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| Author: | Florent Chuffart | |
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+---------------+---------------------------------------------------+ |
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| Version: | 2.3.32 |
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| Version: | 2.3.33 |
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+---------------+---------------------------------------------------+ |
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| License: | CeCILL | |
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+---------------+---------------------------------------------------+ |
| ... | ... | |
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plot_arrow_raw_reads = TRUE, plot_arrow_nuc_reads = TRUE, |
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plot_squared_reads = TRUE, plot_coverage = FALSE, plot_gaussian_reads = TRUE, |
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plot_gaussian_unified_reads = TRUE, plot_ellipse_nucs = TRUE, |
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change_col = TRUE, plot_wp_nucs = TRUE, plot_wp_nuc_model = TRUE,
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plot_common_nucs = TRUE, plot_wp_nucs_4_nonmnase = FALSE,
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plot_chain = FALSE, aggregated_intra_strain_nucs = NULL, |
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change_col = TRUE, plot_wp_nucs = TRUE, plot_fuzzy_nucs = TRUE,
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plot_wp_nuc_model = TRUE, plot_common_nucs = FALSE, plot_common_unrs = FALSE,
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plot_wp_nucs_4_nonmnase = FALSE, plot_chain = FALSE, aggregated_intra_strain_nucs = NULL,
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aligned_inter_strain_nucs = NULL, height = 10, config = NULL) |
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Arguments |
| ... | ... | |
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Plot (or not) cluster of nucs |
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``plot_fuzzy_nucs`` |
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Plot (or not) cluster of fuzzy |
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``plot_wp_nuc_model`` |
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Plot (or not) gaussian model for a cluster of nucs |
| ... | ... | |
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Plot (or not) aligned reads. |
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``plot_common_unrs`` |
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Plot (or not) unaligned nucleosomal refgions (UNRs). |
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``plot_wp_nucs_4_nonmnase`` |
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Plot (or not) clusters for non inputs samples. |
Formats disponibles : Unified diff