Révision 780f632a doc/sphinx_doc/rref.rst
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} |
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print(align_inter_strain_nucs(replicates)) |
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R: Launch DESeq methods.
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R: Compute the list of SNEPs for a given set of marker, strain...
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Launch DESeq methods.
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--------------------- |
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Compute the list of SNEPs for a given set of marker, strain combination and nuc form.
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-------------------------------------------------------------------------------------
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Description |
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~~~~~~~~~~~ |
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This function is based on DESeq example. It normalizes data, fit data to |
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GLM model with and without interaction term and compares the two models. |
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This function uses |
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Usage |
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~~~~~ |
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:: |
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analyse_design(snep_design, reads) |
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analyse_count_table(marker, combi, form, all_samples, |
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FDR = 1e-04, config = NULL) |
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Arguments |
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~~~~~~~~~ |
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``snep_design`` |
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``marker`` |
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The marker involved. |
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``combi`` |
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The design to consider.
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The strain combination involved.
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``reads`` |
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``form`` |
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the nuc form involved. |
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``all_samples`` |
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Global list of samples. |
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``FDR`` |
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The data to consider. |
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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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Examples |
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~~~~~~~~ |
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:: |
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marker = "H3K4me1" |
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combi = c("BY", "YJM")
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form = "wpunr" # "wp" | "unr" | "wpunr" |
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# foo = analyse_count_table(marker, combi, form) |
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# foo = analyse_count_table("H4K12ac", c("BY", "RM"), "wp")
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R: Build count table for a set of samples. |
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Build count table for a set of samples. |
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:: |
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build_count_table(marker, combi, form, curs, config = NULL) |
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build_count_table(marker, combi, form, curs, all_samples, |
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config = NULL) |
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Arguments |
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~~~~~~~~~ |
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The list of CURs |
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``all_samples`` |
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A table that describe all our samples. |
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``config`` |
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GLOBAL config variable. |
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:: |
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compute_inter_all_strain_curs(diff_allowed = 30, min_cur_width = 4000,
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compute_curs(diff_allowed = 30, min_cur_width = 4000, |
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combis = list(c("BY", "RM"), c("BY", "YJM"), c("RM",
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"YJM")), config = NULL) |
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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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------------------------------------------------------------------------------------- |
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Description |
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~~~~~~~~~~~ |
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This function uses |
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Usage |
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~~~~~ |
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:: |
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get_sneps(marker, combi, form, all_samples, FDR = 1e-04, |
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config = NULL) |
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Arguments |
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~~~~~~~~~ |
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``marker`` |
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The marker involved. |
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``combi`` |
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The strain combination involved. |
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``form`` |
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the nuc form involved. |
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``all_samples`` |
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Global list of samples. |
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``FDR`` |
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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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Examples |
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~~~~~~~~ |
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:: |
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marker = "H3K4me1" |
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combi = c("BY", "YJM")
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form = "wpunr" # "wp" | "unr" | "wpunr" |
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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). |
Formats disponibles : Unified diff