[med-svn] [r-bioc-edger] branch master updated (2a03d05 -> b5e9cd8)
Andreas Tille
tille at debian.org
Fri Oct 28 08:36:56 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository r-bioc-edger.
from 2a03d05 Upload to unstable
new 3b301b7 Imported Upstream version 3.16.1+dfsg
new 6ba82ad Merge tag 'upstream/3.16.1+dfsg'
new 5d6830b New upstream version
new a67fc8a Switch to dh-r
new 5ff5298 Adapt patches
new f45bf60 Generic BioConductor homepage
new b5e9cd8 Seems to really need locfit which is default method in some functions
The 7 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
DESCRIPTION | 10 +-
NAMESPACE | 3 +-
R/DGEList.R | 15 +-
R/addPriorCount.R | 27 +
R/adjustedProfileLik.R | 68 +-
R/aveLogCPM.R | 60 +-
R/cpm.R | 25 +-
R/diffSpliceDGE.R | 5 +-
R/estimateDisp.R | 82 +-
R/expandAsMatrix.R | 18 +-
R/glmQLFTest.R | 61 +-
R/glmTreat.R | 131 ++-
R/glmfit.R | 15 +-
R/locfitByCol.R | 5 +-
R/makeCompressedMatrix.R | 164 ++++
R/mglmLevenberg.R | 60 +-
R/mglmOneGroup.R | 36 +-
R/mglmOneWay.R | 29 +-
R/nbinomDeviance.R | 50 +-
R/plotMD.R | 13 +-
R/predFC.R | 34 +-
R/readDGE.R | 18 +-
R/spliceVariants.R | 10 +-
build/vignette.rds | Bin 228 -> 229 bytes
debian/changelog | 10 +
debian/control | 11 +-
debian/copyright | 8 +-
debian/patches/do_not_attempt_locfit_test.patch | 38 +-
debian/rules | 18 +-
inst/CITATION | 37 +-
inst/NEWS.Rd | 39 +
inst/doc/edgeR.pdf | Bin 48664 -> 45765 bytes
man/addPriorCount.Rd | 52 ++
man/aveLogCPM.Rd | 4 +-
man/edgeR-package.Rd | 25 +-
man/estimateDisp.Rd | 5 +-
man/expandAsMatrix.Rd | 21 +-
man/glmQLFTest.Rd | 21 +-
man/glmTreat.Rd | 20 +-
man/goodTuring.Rd | 6 +-
man/makeCompressedMatrix.Rd | 108 +++
man/plotMD.Rd | 3 +
man/plotQLDisp.Rd | 11 +-
man/plotSmear.Rd | 17 +-
man/predFC.Rd | 7 +-
man/processAmplicons.Rd | 34 +-
src/R_add_prior_count.cpp | 64 ++
src/R_add_repeat_matrices.cpp | 41 +
src/R_ave_log_cpm.cpp | 62 ++
src/R_calculate_cpm.cpp | 86 ++
src/R_check_counts.cpp | 137 +++
src/R_check_poisson_bound.cpp | 50 ++
src/R_compute_apl.cpp | 111 +++
src/R_compute_nbdev.cpp | 113 ++-
src/R_cr_adjust.cpp | 43 -
src/R_get_one_way_fitted.cpp | 60 ++
src/R_initialize_levenberg.cpp | 206 +++++
src/R_levenberg.cpp | 105 +--
src/R_one_group.cpp | 136 +--
src/add_prior.cpp | 56 ++
src/add_prior.h | 25 +
src/adj_coxreid.cpp | 62 +-
src/glm.h | 17 +-
src/glm_levenberg.cpp | 120 +--
src/glm_one_group.cpp | 20 +-
src/init.cpp | 24 +-
src/matvec_check.cpp | 178 ++--
src/matvec_check.h | 32 +-
src/nbdev.cpp | 2 +-
src/utils.h | 42 +-
tests/edgeR-Tests.Rout.save | 1079 ++++++++++++-----------
71 files changed, 2886 insertions(+), 1419 deletions(-)
create mode 100644 R/addPriorCount.R
create mode 100644 R/makeCompressedMatrix.R
create mode 100644 man/addPriorCount.Rd
create mode 100644 man/makeCompressedMatrix.Rd
create mode 100644 src/R_add_prior_count.cpp
create mode 100644 src/R_add_repeat_matrices.cpp
create mode 100644 src/R_ave_log_cpm.cpp
create mode 100644 src/R_calculate_cpm.cpp
create mode 100644 src/R_check_counts.cpp
create mode 100644 src/R_check_poisson_bound.cpp
create mode 100644 src/R_compute_apl.cpp
delete mode 100644 src/R_cr_adjust.cpp
create mode 100644 src/R_get_one_way_fitted.cpp
create mode 100644 src/R_initialize_levenberg.cpp
create mode 100644 src/add_prior.cpp
create mode 100644 src/add_prior.h
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