| 199 |
199 |
|
| 200 |
200 |
|
| 201 |
201 |
filter_tf_outputs = function(# Filter TemplateFilter outputs
|
| 202 |
|
### This function filters TemplateFilter outputs according, not only genome area observerved properties, but also correlation and overlap threshold.
|
|
202 |
### This function filters TemplateFilter outputs according, not only genome area observerved properties, but also correlation and overlapping threshold.
|
| 203 |
203 |
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) {
|
| 327 |
|
# print(sample$roi$chr)
|
| 328 |
|
# print(min_nuc_center)
|
| 329 |
|
# print(max_nuc_center)
|
| 330 |
|
# print(sample$outputs)
|
| 331 |
|
# tf_outs[[i]] = filter_tf_outputs(sample$outputs, sample$roi$chr, min_nuc_center, max_nuc_center)
|
| 332 |
|
# print(tf_outs[[i]])
|
| 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
|
| 585 |
|
if (llr_score < llr_thres) {
|
|
579 |
# if (llr_score < llr_thres) {
|
|
580 |
if (TRUE) {
|
| 586 |
581 |
tmp_nuc = list()
|
| 587 |
582 |
# strain_ref1
|
| 588 |
583 |
tmp_nuc[[paste("chr_", strain_ref1, sep="")]] = chr
|
| ... | ... | |
| 592 |
587 |
tmp_nuc[[paste("sd_", strain_ref1, sep="")]] = signif(sd(reads_strain_ref1),5)
|
| 593 |
588 |
tmp_nuc[[paste("nb_reads_", strain_ref1, sep="")]] = length(reads_strain_ref1)
|
| 594 |
589 |
tmp_nuc[[paste("index_nuc_", strain_ref1, sep="")]] = index_nuc_strain_ref1
|
| 595 |
|
# tmp_nuc[[paste("corr1_", strain_ref1, sep="")]] = signif(nuc_strain_ref1$nucs[[1]]$corr,5)
|
| 596 |
|
# tmp_nuc[[paste("corr2_", strain_ref1, sep="")]] = signif(nuc_strain_ref1$nucs[[2]]$corr,5)
|
| 597 |
|
# tmp_nuc[[paste("corr3_", strain_ref1, sep="")]] = signif(nuc_strain_ref1$nucs[[3]]$corr,5)
|
| 598 |
590 |
# strain_ref2
|
| 599 |
591 |
tmp_nuc[[paste("chr_", strain_ref2, sep="")]] = roi_strain_ref2$chr
|
| 600 |
592 |
tmp_nuc[[paste("lower_bound_", strain_ref2, sep="")]] = nuc_strain_ref2$lower_bound
|
| ... | ... | |
| 603 |
595 |
tmp_nuc[[paste("sd_", strain_ref2, sep="")]] = signif(sd(reads_strain_ref2),5)
|
| 604 |
596 |
tmp_nuc[[paste("nb_reads_", strain_ref2, sep="")]] = length(reads_strain_ref2)
|
| 605 |
597 |
tmp_nuc[[paste("index_nuc_", strain_ref2, sep="")]] = index_nuc_strain_ref2
|
| 606 |
|
# tmp_nuc[[paste("corr1_", strain_ref2, sep="")]] = signif(nuc_strain_ref2$nucs[[1]]$corr,5)
|
| 607 |
|
# tmp_nuc[[paste("corr2_", strain_ref2, sep="")]] = signif(nuc_strain_ref2$nucs[[2]]$corr,5)
|
| 608 |
|
# tmp_nuc[[paste("corr3_", strain_ref2, sep="")]] = signif(nuc_strain_ref2$nucs[[3]]$corr,5)
|
| 609 |
598 |
# common
|
| 610 |
599 |
tmp_nuc[["llr_score"]] = signif(llr_score,5)
|
| 611 |
|
# print(tmp_nuc)
|
| 612 |
600 |
common_nuc = dfadd(common_nuc, tmp_nuc)
|
| 613 |
|
}
|
|
601 |
}
|
| 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
|
| 2048 |
|
lines(new_tmp_x , new_tmp_y, lw=2)
|
|
2036 |
lines(new_tmp_x , new_tmp_y, lwd=2)
|
| 2049 |
2037 |
points(tmp_x, tmp_y, cex=4, pch=16, col="white")
|
| 2050 |
|
points(tmp_x, tmp_y, cex=4, lw=2)
|
|
2038 |
points(tmp_x, tmp_y, cex=4, lwd=2)
|
| 2051 |
2039 |
text(tmp_x, tmp_y, 1:nrow(tf_nucs))
|
| 2052 |
2040 |
if (is.null(config$LEGEND_LOD_POS)) {
|
| 2053 |
2041 |
pos = 2
|
| ... | ... | |
| 2148 |
2136 |
common_nuc_results = list()
|
| 2149 |
2137 |
common_nuc_results[[paste(combi[1], combi[2], sep="_")]] = aligned_inter_strain_nucs
|
| 2150 |
2138 |
unrs = get_unrs(combi, roi, cur_index, wp_maps, fuzzy_maps, common_nuc_results, config = config)
|
| 2151 |
|
rect(sign(x_min[[1]]) * unrs$lower_bound + shift[[1]], y_min[[1]], sign(x_min[[1]]) * unrs$upper_bound + shift[[1]], y_max[[2]], border=4, lw=10, col=adjustcolor(4, alpha.f = 0.05))
|
|
2139 |
rect(sign(x_min[[1]]) * unrs$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))
|
| 2152 |
2140 |
}
|
| 2153 |
2141 |
|
| 2154 |
2142 |
}
|