Diffusion functions (master) History

History
master6388e9e8b2957d827b64376…

Jan 5 2021

removed the whole summary from the result of getSignifActivities.R
6388e9e8b295
·pulver on Jan 5 2021, 14:20.

Jan 4 2021

started new sample string
7faa6aa4bff3
·pulver on Jan 4 2021, 12:06.
treatment and control groups added to the ouptut of getSignifActivities
6b73088ced3f
·pulver on Jan 4 2021, 10:19.

Dec 16 2020

added gc() to free memory during preprocess_E_N
45179506f662
·pulver on Dec 16 2020, 16:40.
corrected index bug for N_concat
f2878aa0a65c
·pulver on Dec 16 2020, 15:37.

Dec 14 2020

added getSignifActivities.R
d1d772f30198
·pulver on Dec 14 2020, 15:54.
column centering E before row-centering
f7db3c4ae278
·pulver on Dec 14 2020, 12:54.

Oct 5 2020

correcting broadcasting error in get_pseudocounts
bececb767f56
·pulver on Oct 5 2020, 17:09.

Oct 2 2020

giving N, plotting log tpm
d4ff7541dee4
·pulver on Oct 2 2020, 16:03.
preprocessing of E and N automatic
3d8460088d95
·pulver on Oct 2 2020, 15:43.
row_center.R
009fa13b09e5
·pulver on Oct 2 2020, 14:51.
get_pseudocounts.R
b2f5e5c3acba
·pulver on Oct 2 2020, 14:49.

Sep 28 2020

getActivities with single lambda value across samples
3fc7a956c985
·pulver on Sep 28 2020, 19:19.

Sep 24 2020

do not correct names of predictors
b0befcd88f65
·pulver on Sep 24 2020, 14:47.

Sep 16 2020

typos
a3ee0478f38a
·pulver on Sep 16 2020, 14:38.
removing goldenpath link causing crash
8aa38fb18466
·pulver on Sep 16 2020, 14:38.
tyding up get_tpm.R
40a28e5bfd2c
·pulver on Sep 16 2020, 14:09.
tydied up get_tpm.R
3ebba925f3ad
·pulver on Sep 16 2020, 11:13.
get_tpm in separate file
49baf4cb6710
·pulver on Sep 16 2020, 10:51.

Sep 15 2020

typo
3f1e68b9bacd
·pulver on Sep 15 2020, 14:34.
getActivities log ID
351a1bdc9336
·pulver on Sep 15 2020, 13:35.
ylim on plotActivities
3f5290bdbc76
·pulver on Sep 15 2020, 10:31.

Apr 22 2020

size of labels plotActivities
1c05ceb60837
·pulver on Apr 22 2020, 17:18.

Apr 16 2020

cvsd rename in res list
b3bb144caa65
·pulver on Apr 16 2020, 13:39.
cvsd fix indexing problem
0df5e1dc3da4
·pulver on Apr 16 2020, 13:36.
added cv error and cv std to the result lists of getActivities
6893a2a12861
·pulver on Apr 16 2020, 10:28.
added lamba_min to the return of getActivities
2ef96af9c686
·pulver on Apr 16 2020, 10:15.

Apr 15 2020

camelCap getActivities
48057c61b909
·pulver on Apr 15 2020, 15:31.

Apr 9 2020

corrected perspectives
1d8d54950a2f
·pulver on Apr 9 2020, 19:47.
plotActivities
d4a2d7ac5a71
·pulver on Apr 9 2020, 18:29.
TPM mappable normalization not finished
c66180c8bfd1
·pulver on Apr 9 2020, 09:47.

Apr 6 2020

simple parallel with 1 core per glmnet instance, no parallel on CV
5f9fd1c6fd93
·pulver on Apr 6 2020, 19:33.

Apr 3 2020

default k fold = 5
f7804fe4fb09
·pulver on Apr 3 2020, 19:25.
clean output as list of r2 and activities for get_activities
cecfd2d4e51d
·pulver on Apr 3 2020, 18:56.

Mar 24 2020

get_coefficients polished and tested on sample matrices. Not confirmed on whole…
15c3143b1f5d
·pulver on Mar 24 2020, 17:38.

Mar 23 2020

get_coefficients for ISMARA like TF activity analysis, doesnt run yet
2c9dca0a3566
·pulver on Mar 23 2020, 18:43.

Mar 16 2020

corrected high leverage function to work with hat and not hatvalues (predictor…
9c18b24957b9
·pulver on Mar 16 2020, 19:26.
bullshit function purge high leverage points and aliases lm()
06f2b57d66dd
·pulver on Mar 16 2020, 18:39.
get aliased predictors from lm()
998681712f0b
·pulver on Mar 16 2020, 15:39.
fixed conflict caused by --amend after push for high leverage points
30705d0969a7
·pulver on Mar 16 2020, 10:38.
high leverage points
2210fb6c958f
·pulver on Mar 16 2020, 10:13.
high leverage points
894d5020d0d8
·pulver on Mar 16 2020, 10:01.

Mar 11 2020

R function source file get_TPM and correlation heatmap
fd2803c34f0a
·pulver on Mar 11 2020, 09:14.