| 470 |
470 |
strain_ref1 = replicates[[1]][[1]]$strain
|
| 471 |
471 |
strain_ref2 = replicates[[2]][[1]]$strain
|
| 472 |
472 |
big_roi = replicates[[1]][[1]]$roi
|
|
473 |
orig_big_roi = replicates[[1]][[1]]$orig_roi
|
| 473 |
474 |
if(big_roi$end - big_roi$begin < 0) {
|
| 474 |
475 |
tmp_begin = big_roi$begin
|
| 475 |
476 |
big_roi$begin = big_roi$end
|
| 476 |
477 |
big_roi$end = tmp_begin
|
| 477 |
478 |
}
|
| 478 |
|
tr_big_roi = translate_roi(big_roi, strain_ref2, config=config)
|
| 479 |
|
if(tr_big_roi$end - tr_big_roi$begin < 0) {
|
| 480 |
|
tr_tmp_begin = tr_big_roi$begin
|
| 481 |
|
tr_big_roi$begin = tr_big_roi$end
|
| 482 |
|
tr_big_roi$end = tr_tmp_begin
|
| 483 |
|
}
|
| 484 |
|
# print(big_roi)
|
| 485 |
479 |
# GO!
|
| 486 |
480 |
if (is.null(wp_nucs_strain_ref1)) {
|
| 487 |
481 |
wp_nucs_strain_ref1 = aggregate_intra_strain_nucs(replicates[[1]], ...)[[1]]
|
| ... | ... | |
| 510 |
504 |
# Filtering on Well Positionned
|
| 511 |
505 |
if (nuc_strain_ref1$wp) {
|
| 512 |
506 |
roi_strain_ref1 = list(name=paste("strain_chr_id_" , strain_ref1 , "_" , chr , "_" , "i" , "_", sep=""), begin=nuc_strain_ref1$lower_bound, end=nuc_strain_ref1$upper_bound, chr=chr, strain_ref = strain_ref1)
|
| 513 |
|
roi_strain_ref2 = translate_roi(roi_strain_ref1, strain_ref2, big_roi=big_roi, config=config)
|
|
507 |
roi_strain_ref2 = translate_roi(roi_strain_ref1, strain_ref2, big_roi=orig_big_roi, config=config)
|
| 514 |
508 |
if (!is.null(roi_strain_ref2)){
|
| 515 |
509 |
# LOADING INTRA_STRAIN_NUCS_FILENAME_STRAIN_REF2 FILE(S) TO COMPUTE MATCHING_NAS (FILTER)
|
| 516 |
510 |
lower_bound_roi_strain_ref2 = min(roi_strain_ref2$end,roi_strain_ref2$begin)
|
| ... | ... | |
| 520 |
514 |
nuc_strain_ref2 = wp_nucs_strain_ref2[[index_nuc_strain_ref2]]
|
| 521 |
515 |
# Filtering on Well Positionned
|
| 522 |
516 |
nuc_strain_ref2_to_roi = list(begin=nuc_strain_ref2$lower_bound, end=nuc_strain_ref2$upper_bound, chr=nuc_strain_ref2$chr, strain_ref = strain_ref2)
|
| 523 |
|
if (!(tr_big_roi$chr!=nuc_strain_ref2$chr |
|
| 524 |
|
nuc_strain_ref2$upper_bound > tr_big_roi$end |
|
| 525 |
|
nuc_strain_ref2$upper_bound < tr_big_roi$begin |
|
| 526 |
|
nuc_strain_ref2$lower_bound > tr_big_roi$end |
|
| 527 |
|
nuc_strain_ref2$lower_bound < tr_big_roi$begin) &
|
| 528 |
|
!is.null(translate_roi(nuc_strain_ref2_to_roi, strain_ref1, big_roi=big_roi, config=config)) &
|
|
517 |
if (!is.null(translate_roi(nuc_strain_ref2_to_roi, strain_ref1, big_roi=orig_big_roi, config=config)) &
|
| 529 |
518 |
nuc_strain_ref2$wp) {
|
| 530 |
519 |
# Filtering on correlation Score and collecting reads
|
| 531 |
520 |
SKIP = FALSE
|
| ... | ... | |
| 707 |
696 |
samples_ids = unique(all_samples[all_samples$marker == "Mnase_Seq" & all_samples$strain == strain,]$id)
|
| 708 |
697 |
for (i in samples_ids) {
|
| 709 |
698 |
sample = as.list(all_samples[all_samples$id==i,])
|
|
699 |
sample$orig_roi = roi
|
| 710 |
700 |
sample$roi = translate_roi(roi, sample$strain, config = config)
|
| 711 |
701 |
if (get_genome) {
|
| 712 |
702 |
# Get Genome
|
| ... | ... | |
| 1781 |
1771 |
samples=list()
|
| 1782 |
1772 |
for (i in samples_ids) {
|
| 1783 |
1773 |
sample = as.list(all_samples[all_samples$id==i,])
|
|
1774 |
sample$orig_roi = roi
|
| 1784 |
1775 |
sample$roi = translate_roi(roi, sample$strain, config = config)
|
| 1785 |
1776 |
if (get_genome) {
|
| 1786 |
1777 |
# Get Genome
|