-
Notifications
You must be signed in to change notification settings - Fork 4
/
UPDATES
54 lines (53 loc) · 3.37 KB
/
UPDATES
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
1.0.8:
Reversed compatibility warning due to lack of schedule for version 2.
1.0.7:
Added compatibility warning for interface changes in future versions.
1.0.6:
Corrected a bug that may produce biased output in pij_gassist, pij_gassist_trad, and pijs_gassist when nodiag is set or when memlimit is small so computation is split into chunks.
Now setting histogram bounds based on the maximum of all LLRs (as opposed to the maximum of the chunk when memlimit is small) in pij_gassist, pij_gassist_trad, and pijs_gassist. This ensures the output is independent of memlimit (related to question from sritchie73@github).
Added sanity checks for agreement between input data and nodiag flag for pij functions excluding _pv (suggested by sritchie73@github).
Lots of internal function renaming and code restructuring.
Removed some unneeded files and functions.
Now support pkg-config setup.
1.0.5:
Updated Makefiles to account for different make environments (reported by sritchie73@github).
1.0.1:
Bug correction:
Updated LDFLAGS for R interface (reported by audreyqyfu@github).
1.0.0:
New functions:
Included P-value computation for 4 tests in pijs_gassist_pv and correlation test in pij_rank_pv.
Included using continuous anchors (instead of discrete genotypes) for causal inference in pij(s)_cassist*.
Revisions:
Minor adjustments on adding fluctuations for supernormalized data when the number of samples is small (<30).
Updated logging.
Minor adjustments in conversion from LLR to local FDR.
Minor bug corrections on defensive programming.
0.5.0:
New function: reconstruction of directed acyclic graph from prior information of edge significance. For details, see library function netr_one_greedy, doc.pdf, or UPDATES in any interface.
0.4.1:
Extreme situation behavior:
Added error checking for few samples (<4).
Added special consideration for extremely skewed LLR during local FDR estimation.
Updated copyright notice.
0.4.0:
Interface changes:
Removed trailing _a's for all interface function names.
Removed _tot functions. (See Obsoletes.)
Binary interface has an extra parameter specifying memory usage limit.
Python interface has an optional parameter specifying memory usage limit.
Improvements:
We have introduced the function pij_gassist_trad for traditional inference test.
We have parallelized the remaining part of major computation and obtained even faster speed.
We have modified functions to perform inplace operations as much as possible to save memory.
We have introduced memory usage limit as a parameter (except R interface). Large datasets will be automatically split before calculation to keep memory usage under limit.
We have included p1 calculation for nodiag=1 case.
Better input validity checks for interfaces.
Bug corrections.
Obsoletes:
In order to reduce effort in improving and maintaining the package, we decided to obsolete several non-essential functions. They include:
pij(s)_*_tot functions: they will be hardly needed as more genes can be measured by advancing technologies.
Windows native support: The latest version of Windows has provided support for Ubuntu Bash. All interfaces should integrate better with Bash on Windows. (https://msdn.microsoft.com/commandline/wsl)
0.3.0:
Function pijs_gassist_*: changed function definition to provide latest test statistics.
Function pij_gassist_*: added new funciton for recommended combination of tests.