Révision b20637ed
| b/doc/sphinx_doc/build/text/tuto.txt | ||
|---|---|---|
| 384 | 384 |
steps. |
| 385 | 385 |
|
| 386 | 386 |
The second part of the tutoriel use *R* |
| 387 |
(http://http://www.r-project.org). It consists in the 3 main steps
|
|
| 388 |
corresponding to 4 R scripts:
|
|
| 387 |
(http://http://www.r-project.org). It consists in the following main
|
|
| 388 |
steps:
|
|
| 389 | 389 |
|
| 390 | 390 |
* compute_rois.R |
| 391 | 391 |
|
| 392 | 392 |
* extract_maps.R |
| 393 | 393 |
|
| 394 |
* compare_common_wp.R |
|
| 395 |
|
|
| 396 |
* split_samples.R |
|
| 397 |
|
|
| 394 | 398 |
* count_reads.R |
| 395 | 399 |
|
| 396 | 400 |
* get_size_factors |
| ... | ... | |
| 410 | 414 |
R CMD BATCH src/current/extract_maps.R |
| 411 | 415 |
|
| 412 | 416 |
|
| 417 |
Compute Distance Between Well Positionned Nucleosomes |
|
| 418 |
----------------------------------------------------- |
|
| 419 |
|
|
| 420 |
R CMD BATCH src/current/compare_common_wp.R |
|
| 421 |
|
|
| 422 |
|
|
| 423 |
Split and Compress Samples According CURs |
|
| 424 |
----------------------------------------- |
|
| 425 |
|
|
| 426 |
R CMD BATCH src/current/split_samples.R |
|
| 427 |
|
|
| 428 |
|
|
| 413 | 429 |
Count Reads for Each Nucleosome |
| 414 | 430 |
------------------------------- |
| 415 | 431 |
|
| b/doc/sphinx_doc/conf.py | ||
|---|---|---|
| 50 | 50 |
# built documents. |
| 51 | 51 |
# |
| 52 | 52 |
# The short X.Y version. |
| 53 |
version = '2.3.18'
|
|
| 53 |
version = '2.3.19'
|
|
| 54 | 54 |
# The full version, including alpha/beta/rc tags. |
| 55 |
release = '2.3.18'
|
|
| 55 |
release = '2.3.19'
|
|
| 56 | 56 |
|
| 57 | 57 |
# The language for content autogenerated by Sphinx. Refer to documentation |
| 58 | 58 |
# for a list of supported languages. |
| b/doc/sphinx_doc/rref.rst | ||
|---|---|---|
| 1114 | 1114 |
+---------------+---------------------------------------------------+ |
| 1115 | 1115 |
| Author: | Florent Chuffart | |
| 1116 | 1116 |
+---------------+---------------------------------------------------+ |
| 1117 |
| Version: | 2.3.18 |
|
|
| 1117 |
| Version: | 2.3.19 |
|
|
| 1118 | 1118 |
+---------------+---------------------------------------------------+ |
| 1119 | 1119 |
| License: | CeCILL | |
| 1120 | 1120 |
+---------------+---------------------------------------------------+ |
| b/doc/sphinx_doc/tuto.rst | ||
|---|---|---|
| 297 | 297 |
|
| 298 | 298 |
|
| 299 | 299 |
The second part of the tutoriel use `R` (http://http://www.r-project.org). It |
| 300 |
consists in the 3 main steps corresponding to 4 R scripts:
|
|
| 300 |
consists in the following main steps:
|
|
| 301 | 301 |
|
| 302 | 302 |
- compute_rois.R |
| 303 | 303 |
- extract_maps.R |
| 304 |
- compare_common_wp.R |
|
| 305 |
- split_samples.R |
|
| 304 | 306 |
- count_reads.R |
| 305 | 307 |
- get_size_factors |
| 306 | 308 |
- launch_deseq.R |
| ... | ... | |
| 321 | 323 |
R CMD BATCH src/current/extract_maps.R |
| 322 | 324 |
|
| 323 | 325 |
|
| 326 |
Compute Distance Between Well Positionned Nucleosomes |
|
| 327 |
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
|
| 328 |
|
|
| 329 |
.. code:: bash |
|
| 330 |
|
|
| 331 |
R CMD BATCH src/current/compare_common_wp.R |
|
| 332 |
|
|
| 333 |
|
|
| 334 |
Split and Compress Samples According CURs |
|
| 335 |
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
|
| 336 |
|
|
| 337 |
.. code:: bash |
|
| 338 |
|
|
| 339 |
R CMD BATCH src/current/split_samples.R |
|
| 340 |
|
|
| 341 |
|
|
| 324 | 342 |
Count Reads for Each Nucleosome |
| 325 | 343 |
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
| 326 | 344 |
|
| b/src/DESCRIPTION | ||
|---|---|---|
| 1 | 1 |
Package: nucleominer |
| 2 | 2 |
Maintainer: Florent Chuffart <florent.chuffart@ens-lyon.fr> |
| 3 | 3 |
Author: Florent Chuffart |
| 4 |
Version: 2.3.18
|
|
| 4 |
Version: 2.3.19
|
|
| 5 | 5 |
License: CeCILL |
| 6 | 6 |
Title: nm |
| 7 | 7 |
Depends: seqinr, plotrix, DESeq, cachecache |
| b/src/R/nucleominer.R | ||
|---|---|---|
| 767 | 767 |
} |
| 768 | 768 |
non_inter_fuzzy = rec_substract_region(region1, region2) |
| 769 | 769 |
if (is.null(non_inter_fuzzy)) {return(non_inter_fuzzy)}
|
| 770 |
return(collapse_regions(non_inter_fuzzy)) |
|
| 770 |
tmp_ulist = unlist(non_inter_fuzzy) |
|
| 771 |
tmp_names = names(tmp_ulist)[1:4] |
|
| 772 |
non_inter_fuzzy = data.frame(matrix(tmp_ulist, ncol=4, byrow=TRUE), stringsAsFactors=FALSE) |
|
| 773 |
names(non_inter_fuzzy) = tmp_names |
|
| 774 |
non_inter_fuzzy$chr = as.character(non_inter_fuzzy$chr) |
|
| 775 |
non_inter_fuzzy$chr = as.numeric(non_inter_fuzzy$chr) |
|
| 776 |
non_inter_fuzzy$lower_bound = as.numeric(non_inter_fuzzy$lower_bound) |
|
| 777 |
non_inter_fuzzy$upper_bound = as.numeric(non_inter_fuzzy$upper_bound) |
|
| 778 |
non_inter_fuzzy = non_inter_fuzzy[order(non_inter_fuzzy$lower_bound),] |
|
| 779 |
return(non_inter_fuzzy) |
|
| 771 | 780 |
} |
| 772 | 781 |
|
| 773 | 782 |
union_regions = function(# Aggregate regions that intersect themnselves. |
| ... | ... | |
| 841 | 850 |
### Utils to reformat an "apply manipulated" list of regions |
| 842 | 851 |
regions ##< a list of regions |
| 843 | 852 |
) {
|
| 844 |
regions = do.call("rbind", regions)
|
|
| 853 |
regions = do.call(rbind, regions)
|
|
| 845 | 854 |
regions$chr = as.character(regions$chr) |
| 846 | 855 |
regions$chr = as.numeric(regions$chr) |
| 847 | 856 |
regions$lower_bound = as.numeric(regions$lower_bound) |
Formats disponibles : Unified diff