1. crlmm
  2. inst
  3. scripts
  4. sync
Browse code

commit after bioc rebase

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52859 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 16:19:11
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-rsync -avuzb --exclude '*~' --exclude 'ffobjs*' --exclude '.git*' -e ssh ~/madman/Rpacks/git/crlmm/ enigma2.jhsph.edu:~/madman/Rpacks/git/crlmm
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-rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh enigma2.jhsph.edu:~/madman/Rpacks/git/crlmm/inst/scripts/*opynumber.pdf ~/madman/Rpacks/git/crlmm/inst/scripts/
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+rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh ~/madman/Rpacks/git/crlmm/ enigma2.jhsph.edu:~/madman/Rpacks/git/crlmm
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+rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm/inst/scripts/*opynumber.pdf ~/madman/Rpacks/git/crlmm/inst/scripts/
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Browse code

Comment open and close statements in stripnormalize

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52850 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 15:59:16
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-rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh ~/madman/Rpacks/git/crlmm/ enigma2.jhsph.edu:~/madman/Rpacks/git/crlmm
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-rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm/inst/scripts/*opynumber.pdf ~/madman/Rpacks/git/crlmm/inst/scripts/
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+rsync -avuzb --exclude '*~' --exclude 'ffobjs*' --exclude '.git*' -e ssh ~/madman/Rpacks/git/crlmm/ enigma2.jhsph.edu:~/madman/Rpacks/git/crlmm
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+rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh enigma2.jhsph.edu:~/madman/Rpacks/git/crlmm/inst/scripts/*opynumber.pdf ~/madman/Rpacks/git/crlmm/inst/scripts/
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Browse code

Finalize updates to copynumber and illumina_copynumber vignettes for v1.8.3 updates

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52837 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 15:58:28
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Browse code

fix for finding index of nonpolymorphic markers in genotype function

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52834 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 15:58:14
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 rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm/inst/scripts/*opynumber.pdf ~/madman/Rpacks/git/crlmm/inst/scripts/
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Browse code

changes to shrinkGenotypeSummarries and C3 function for estimation of copy number at SNPs on chromosome X

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52815 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 15:57:05
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-rsync -avuzb --exclude '~*' --exclude '.git*' -e ssh ~/madman/Rpacks/git/crlmm/ enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm
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-rsync -avuzb --exclude '.git*' -e ssh enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm/inst/scripts/copynumber.pdf ~/madman/Rpacks/git/crlmm/inst/scripts/copynumber.pdf
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+rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh ~/madman/Rpacks/git/crlmm/ enigma2.jhsph.edu:~/madman/Rpacks/git/crlmm
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+rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm/inst/scripts/*opynumber.pdf ~/madman/Rpacks/git/crlmm/inst/scripts/
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Browse code

Bug in copy number accessors fixed.

This fixes a bug that occurs when CA() or CB() for a random subset of
samples with mixed batches was accessed -- the order of samples
returned was incorrect. The dimnames of the resulting object are
returned as well.

copynumber.pdf vignette also updated

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52813 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 15:56:57
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-rsync -avuzb --exclude '.git*' -e ssh ~/madman/Rpacks/git/crlmm/ enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm
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+rsync -avuzb --exclude '~*' --exclude '.git*' -e ssh ~/madman/Rpacks/git/crlmm/ enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm
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+rsync -avuzb --exclude '.git*' -e ssh enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm/inst/scripts/copynumber.pdf ~/madman/Rpacks/git/crlmm/inst/scripts/copynumber.pdf
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Browse code

fix for finding index of nonpolymorphic markers in genotype function

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52811 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 15:56:48
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-rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh ~/madman/Rpacks/git/crlmm/ enigma2.jhsph.edu:~/madman/Rpacks/git/crlmm
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-rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh enigma2.jhsph.edu:~/madman/Rpacks/git/crlmm/inst/scripts/*opynumber.pdf ~/madman/Rpacks/git/crlmm/inst/scripts/
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+rsync -avuzb --exclude '.git*' -e ssh ~/madman/Rpacks/git/crlmm/ enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm
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Browse code

add check for missing.index length in illumina_copynumber vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50901 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 15/11/2010 14:24:50
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 rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh ~/madman/Rpacks/git/crlmm/ enigma2.jhsph.edu:~/madman/Rpacks/git/crlmm
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-rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm/inst/scripts/*opynumber.pdf ~/madman/Rpacks/git/crlmm/inst/scripts/
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+rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh enigma2.jhsph.edu:~/madman/Rpacks/git/crlmm/inst/scripts/*opynumber.pdf ~/madman/Rpacks/git/crlmm/inst/scripts/
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Browse code

changed line in crlmm-illumina function processIDAT. bb <- getOption("ffbatchbytes")

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50897 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 15/11/2010 14:24:24
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-rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh ~/madman/Rpacks/git/crlmm/ enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm
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+rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh ~/madman/Rpacks/git/crlmm/ enigma2.jhsph.edu:~/madman/Rpacks/git/crlmm
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 rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm/inst/scripts/*opynumber.pdf ~/madman/Rpacks/git/crlmm/inst/scripts/
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Browse code

Finalize updates to copynumber and illumina_copynumber vignettes for v1.8.3 updates

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50890 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 15/11/2010 14:22:42
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-rsync -avuzb --exclude '~*' --exclude '.git*' -e ssh ~/madman/Rpacks/git/crlmm/ enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm
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-rsync -avuzb --exclude '.git*' -e ssh enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm/inst/scripts/copynumber.pdf ~/madman/Rpacks/git/crlmm/inst/scripts/copynumber.pdf
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+rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh ~/madman/Rpacks/git/crlmm/ enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm
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+rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm/inst/scripts/*opynumber.pdf ~/madman/Rpacks/git/crlmm/inst/scripts/
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Browse code

Bug in copy number accessors fixed.

This fixes a bug that occurs when CA() or CB() for a random subset of
samples with mixed batches was accessed -- the order of samples
returned was incorrect. The dimnames of the resulting object are
returned as well.

copynumber.pdf vignette also updated

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50889 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 15/11/2010 14:21:58
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-rsync -avuzb --exclude '.git*' -e ssh ~/madman/Rpacks/git/crlmm/ enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm
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+rsync -avuzb --exclude '~*' --exclude '.git*' -e ssh ~/madman/Rpacks/git/crlmm/ enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm
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+rsync -avuzb --exclude '.git*' -e ssh enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm/inst/scripts/copynumber.pdf ~/madman/Rpacks/git/crlmm/inst/scripts/copynumber.pdf
Browse code

fix for finding index of nonpolymorphic markers in genotype function

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50887 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 15/11/2010 14:21:45
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new file mode 100755
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+rsync -avuzb --exclude '.git*' -e ssh ~/madman/Rpacks/git/crlmm/ enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm