Révision ec2936ea src/R/nucleominer.R
| b/src/R/nucleominer.R | ||
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| 199 | 199 |
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| 200 | 200 |
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filter_tf_outputs = function(# Filter TemplateFilter outputs |
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### This function filters TemplateFilter outputs according, not only genome area observerved properties, but also correlation and overlap threshold. |
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### This function filters TemplateFilter outputs according, not only genome area observerved properties, but also correlation and overlapping threshold.
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tf_outputs, ##<< TemplateFilter outputs. |
| 204 | 204 |
chr, ##<< Chromosome observed, here chr is an integer. |
| 205 | 205 |
x_min, ##<< Coordinate of the first bp observed. |
| ... | ... | |
| 324 | 324 |
tf_outs = list() |
| 325 | 325 |
i = 1 |
| 326 | 326 |
for (sample in samples) {
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# print(sample$roi$chr) |
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# print(min_nuc_center) |
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# print(max_nuc_center) |
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# print(sample$outputs) |
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# tf_outs[[i]] = filter_tf_outputs(sample$outputs, sample$roi$chr, min_nuc_center, max_nuc_center) |
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# print(tf_outs[[i]]) |
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| 333 | 327 |
tf_outs[[i]] = sample$outputs |
| 334 | 328 |
tf_outs[[i]] = tf_outs[[i]][order(tf_outs[[i]]$center),] |
| 335 | 329 |
indexes[i] = 1 |
| ... | ... | |
| 582 | 576 |
llr_score = llr_score_nvecs(list(reads_strain_ref1, reads_strain_ref2)) |
| 583 | 577 |
llr_scores = c(llr_scores, llr_score) |
| 584 | 578 |
# Filtering on LOD Score |
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if (llr_score < llr_thres) {
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# if (llr_score < llr_thres) {
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if (TRUE) {
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tmp_nuc = list() |
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# strain_ref1 |
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tmp_nuc[[paste("chr_", strain_ref1, sep="")]] = chr
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| ... | ... | |
| 592 | 587 |
tmp_nuc[[paste("sd_", strain_ref1, sep="")]] = signif(sd(reads_strain_ref1),5)
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| 593 | 588 |
tmp_nuc[[paste("nb_reads_", strain_ref1, sep="")]] = length(reads_strain_ref1)
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| 594 | 589 |
tmp_nuc[[paste("index_nuc_", strain_ref1, sep="")]] = index_nuc_strain_ref1
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# tmp_nuc[[paste("corr1_", strain_ref1, sep="")]] = signif(nuc_strain_ref1$nucs[[1]]$corr,5)
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# tmp_nuc[[paste("corr2_", strain_ref1, sep="")]] = signif(nuc_strain_ref1$nucs[[2]]$corr,5)
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# tmp_nuc[[paste("corr3_", strain_ref1, sep="")]] = signif(nuc_strain_ref1$nucs[[3]]$corr,5)
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| 598 | 590 |
# strain_ref2 |
| 599 | 591 |
tmp_nuc[[paste("chr_", strain_ref2, sep="")]] = roi_strain_ref2$chr
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| 600 | 592 |
tmp_nuc[[paste("lower_bound_", strain_ref2, sep="")]] = nuc_strain_ref2$lower_bound
|
| ... | ... | |
| 603 | 595 |
tmp_nuc[[paste("sd_", strain_ref2, sep="")]] = signif(sd(reads_strain_ref2),5)
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| 604 | 596 |
tmp_nuc[[paste("nb_reads_", strain_ref2, sep="")]] = length(reads_strain_ref2)
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| 605 | 597 |
tmp_nuc[[paste("index_nuc_", strain_ref2, sep="")]] = index_nuc_strain_ref2
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# tmp_nuc[[paste("corr1_", strain_ref2, sep="")]] = signif(nuc_strain_ref2$nucs[[1]]$corr,5)
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# tmp_nuc[[paste("corr2_", strain_ref2, sep="")]] = signif(nuc_strain_ref2$nucs[[2]]$corr,5)
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# tmp_nuc[[paste("corr3_", strain_ref2, sep="")]] = signif(nuc_strain_ref2$nucs[[3]]$corr,5)
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| 609 | 598 |
# common |
| 610 | 599 |
tmp_nuc[["llr_score"]] = signif(llr_score,5) |
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# print(tmp_nuc) |
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| 612 | 600 |
common_nuc = dfadd(common_nuc, tmp_nuc) |
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}
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}
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| 614 | 602 |
} |
| 615 | 603 |
} |
| 616 | 604 |
} |
| ... | ... | |
| 2045 | 2033 |
new_tmp_y[index_odd] = tmp_y |
| 2046 | 2034 |
new_tmp_x[index_even] = tmp_x_inter |
| 2047 | 2035 |
new_tmp_y[index_even] = tmp_y_inter |
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lines(new_tmp_x , new_tmp_y, lw=2) |
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lines(new_tmp_x , new_tmp_y, lwd=2)
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| 2049 | 2037 |
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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points(tmp_x, tmp_y, cex=4, lwd=2)
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| 2051 | 2039 |
text(tmp_x, tmp_y, 1:nrow(tf_nucs)) |
| 2052 | 2040 |
if (is.null(config$LEGEND_LOD_POS)) {
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| 2053 | 2041 |
pos = 2 |
| ... | ... | |
| 2148 | 2136 |
common_nuc_results = list() |
| 2149 | 2137 |
common_nuc_results[[paste(combi[1], combi[2], sep="_")]] = aligned_inter_strain_nucs |
| 2150 | 2138 |
unrs = get_unrs(combi, roi, cur_index, wp_maps, fuzzy_maps, common_nuc_results, config = config) |
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rect(sign(x_min[[1]]) * unrs$lower_bound + shift[[1]], y_min[[1]], sign(x_min[[1]]) * unrs$upper_bound + shift[[1]], y_max[[2]], border=4, lw=10, col=adjustcolor(4, alpha.f = 0.05)) |
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rect(sign(x_min[[1]]) * unrs$lower_bound + shift[[1]], y_min[[1]], sign(x_min[[1]]) * unrs$upper_bound + shift[[1]], y_max[[2]], border=4, lwd=10, col=adjustcolor(4, alpha.f = 0.05))
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| 2152 | 2140 |
} |
| 2153 | 2141 |
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| 2154 | 2142 |
} |
Formats disponibles : Unified diff