Révision 7646593d
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# built documents. |
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# |
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# The short X.Y version. |
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version = '2.3.26'
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version = '2.3.27'
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# The full version, including alpha/beta/rc tags. |
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release = '2.3.26'
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release = '2.3.27'
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# The language for content autogenerated by Sphinx. Refer to documentation |
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# for a list of supported languages. |
| b/doc/sphinx_doc/rref.rst | ||
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Florent Chuffart |
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R: to flat aggregate\_intra\_strain\_nucs function output |
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to flat aggregate\_intra\_strain\_nucs function output |
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------------------------------------------------------ |
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Description |
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~~~~~~~~~~~ |
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This function builds a dataframe of all clusters obtain from |
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aggregate\_intra\_strain\_nucs function. |
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Usage |
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~~~~~ |
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:: |
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flat_aggregated_intra_strain_nucs(partial_strain_maps, roi_index) |
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Arguments |
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~~~~~~~~~ |
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``partial_strain_maps`` |
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the output of aggregate\_intra\_strain\_nucs function |
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``roi_index`` |
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the index of the roi involved |
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Value |
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~~~~~ |
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Returns a dataframe of all clusters obtain from |
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aggregate\_intra\_strain\_nucs function. |
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Author(s) |
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~~~~~~~~~ |
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Florent Chuffart |
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R: flat reads |
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flat reads |
| ... | ... | |
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+---------------+---------------------------------------------------+ |
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| Author: | Florent Chuffart | |
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+---------------+---------------------------------------------------+ |
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| Version: | 2.3.26 |
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| Version: | 2.3.27 |
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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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plot_wp_nucs = TRUE, plot_wp_nuc_model = TRUE, plot_common_nucs = TRUE,
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plot_anovas = FALSE, plot_anova_boxes = FALSE, 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_wp_nuc_model = TRUE,
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plot_common_nucs = TRUE, plot_anovas = FALSE, plot_anova_boxes = 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) ellipse for a nuc. |
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``change_col`` |
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Change the color of each nucleosome. |
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``plot_wp_nucs`` |
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Plot (or not) cluster of nucs |
| b/src/DESCRIPTION | ||
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Package: nucleominer |
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Maintainer: Florent Chuffart <florent.chuffart@ens-lyon.fr> |
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Author: Florent Chuffart |
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Version: 2.3.26
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Version: 2.3.27
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License: CeCILL |
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Title: nm |
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Depends: seqinr, plotrix, DESeq, cachecache |
| b/src/R/nucleominer.R | ||
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print(aggregate_intra_strain_nucs(samples)) |
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}) |
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flat_aggregated_intra_strain_nucs = function(# to flat aggregate_intra_strain_nucs function output |
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### This function builds a dataframe of all clusters obtain from aggregate_intra_strain_nucs function. |
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partial_strain_maps, ##<< the output of aggregate_intra_strain_nucs function |
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roi_index ##<< the index of the roi involved |
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) {
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if (length(partial_strain_maps) == 0 ){
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print(paste("Empty partial_strain_maps for roi", roi_index, "ands strain", strain, "." ))
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tmp_strain_maps = list() |
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} else {
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tmp_strain_map = apply(t(1:length(partial_strain_maps)), 2, function(i){
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tmp_nuc = partial_strain_maps[[i]] |
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tmp_nuc_as_list = list() |
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tmp_nuc_as_list[["chr"]] = tmp_nuc[["chr"]] |
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tmp_nuc_as_list[["lower_bound"]] = ceiling(tmp_nuc[["lower_bound"]]) |
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tmp_nuc_as_list[["upper_bound"]] = floor(tmp_nuc[["upper_bound"]]) |
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tmp_nuc_as_list[["roi_index"]] = roi_index |
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tmp_nuc_as_list[["index_nuc"]] = i |
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tmp_nuc_as_list[["wp"]] = as.integer(tmp_nuc$wp) |
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all_original_reads = c() |
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for (j in 1:length(tmp_nuc$nucs)) {
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all_original_reads = c(all_original_reads, tmp_nuc$nucs[[j]]$original_reads) |
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} |
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tmp_nuc_as_list[["nb_reads"]] = length(all_original_reads) |
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if (tmp_nuc$wp) {
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tmp_nuc_as_list[["lod_1"]] = signif(tmp_nuc$nucs[[2]]$lod_score,5) |
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tmp_nuc_as_list[["lod_2"]] = signif(tmp_nuc$nucs[[3]]$lod_score,5) |
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} else {
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tmp_nuc_as_list[["lod_1"]] = NA |
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tmp_nuc_as_list[["lod_2"]] = NA |
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} |
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return(tmp_nuc_as_list) |
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}) |
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tmp_strain_maps = do.call("rbind", tmp_strain_map)
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} |
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return(data.frame(tmp_strain_maps)) |
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### Returns a dataframe of all clusters obtain from aggregate_intra_strain_nucs function. |
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} |
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align_inter_strain_nucs = structure(function(# Aligns nucleosomes between 2 strains. |
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### This function aligns nucs between two strains for a given genome region. |
| ... | ... | |
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plot_gaussian_reads = TRUE, ##<< Plot (or not) gaussian model of a F anf R reads. |
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plot_gaussian_unified_reads = TRUE, ##<< Plot (or not) gaussian model of a nuc. |
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plot_ellipse_nucs = TRUE, ##<< Plot (or not) ellipse for a nuc. |
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change_col = TRUE, ##<< Change the color of each nucleosome. |
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plot_wp_nucs = TRUE, ##<< Plot (or not) cluster of nucs |
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plot_wp_nuc_model = TRUE, ##<< Plot (or not) gaussian model for a cluster of nucs |
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plot_common_nucs = TRUE, ##<< Plot (or not) aligned reads. |
| ... | ... | |
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if (length(nucs$center) > 0) {
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col = 1 |
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for (i in 1:length(nucs$center)) {
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col = col + 1 |
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if (change_col) {
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col = col + 1 |
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} |
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nuc = nucs[i,] |
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involved_reads = filter_tf_inputs(reads, sample$roi$chr, nuc$lower_bound, nuc$upper_bound, nuc_width = nuc$width) |
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involved_signs = apply(t(involved_reads[,3]), 2, function(strand) { if (strand == "F") return(1) else return(-1)})
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# Plot wp nucs |
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if ((plot_wp_nucs_4_nonmnase | sample$marker == "Mnase_Seq") & (plot_wp_nucs | plot_common_nucs | plot_chain)) {
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if (samples[[1]]$marker == "Mnase_Seq") {
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if (is.null(aggregated_intra_strain_nucs)) {
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if (is.null(aggregated_intra_strain_nucs)) {
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wp_nucs = aggregate_intra_strain_nucs(samples)[[1]] |
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foo <<- wp_nucs |
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} else {
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wp_nucs = aggregated_intra_strain_nucs[[replicate_rank]] |
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} |
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} else {
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wp_nucs = replicates_wp_nucs[[replicate_rank-2]] |
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} |
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if (plot_chain) {
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tf_nucs = lapply(wp_nucs, function(nuc) {
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bar = apply(t(nuc$nucs), 2, function(tmp_nuc){
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| ... | ... | |
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points(tmp_x, tmp_y, cex=4, pch=16, col="white") |
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points(tmp_x, tmp_y, cex=4, lw=2) |
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text(tmp_x, tmp_y, 1:nrow(tf_nucs)) |
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text(tmp_x_inter, tmp_y_inter, tmp_lod_inter, col=(tmp_lod_inter < 20) + 2) |
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text(tmp_x_inter, tmp_y_inter, tmp_lod_inter, srt=90, cex=0.9, bg = "yellow")#, col=(tmp_lod_inter < 20) + 2)
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} |
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if (plot_wp_nucs | plot_common_nucs ) {
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Formats disponibles : Unified diff