March 2, 2011
Viewc75c54c

fixed cyclic namespace dependency by updating version dependencies in DESCRIPTION, and updating other bioc packages

Rob Scharp authored on 02/03/2011 00:59:03
February 16, 2011
View453e688

commit after bioc rebase

Rob Scharp authored on 16/02/2011 16:19:11
View7e59dce

excplicit coercion of A() and B() to matrices in C1, C2, and C3 functions (affect totalCopynumber)

Rob Scharp authored on 16/02/2011 15:59:48
View2fd64c7

add functions to impute centers using cross-batch information

Rob Scharp authored on 16/02/2011 15:59:44
View937a9f3

add open and close statements inside processCEL2. Fix NR in rscrlmmGT2

Rob Scharp authored on 16/02/2011 15:59:37
Viewcaaed0d

genotype now calls 'rscrlmmGT2'. rscrlmmGT2 is a copy of crlmmGT2

Rob Scharp authored on 16/02/2011 15:59:32
View05aaf16

a few edits to rsprocessCEL so that the normalized intensities are written to the appropriate index in A and B

Rob Scharp authored on 16/02/2011 15:59:28
View08d4b4d

copied processCEL to rsprocessCEL. Removed call to snprma2 from genotype function.

Rob Scharp authored on 16/02/2011 15:59:24
View659b963

create function called mycrlmmGT2. comment lines for initializing call and callProbability in construct function

Rob Scharp authored on 16/02/2011 15:59:20
View14c3063

Edit warning message for MIN.SAMPLES

Rob Scharp authored on 16/02/2011 15:58:58
Viewe8871ea

fit.lm4 returns nothing and stops execution if fewer than 100 SNPs meet criteria

Rob Scharp authored on 16/02/2011 15:58:54
View07d00a5

fit.lm4 excludes batches less than MIN.SAMPLES when computing snp.index. Fixed bug in fit.lm3 -- use >= MIN.SAMPLES instead of > MIN.SAMPLES

Rob Scharp authored on 16/02/2011 15:57:54
Viewa966e04

use drop=FALSE in summarizeSnps for batches of size 1

Rob Scharp authored on 16/02/2011 15:57:50
View8decfc7

stopifnot(type != "SNP") changed to stopifnot(type=="SNP")

Rob Scharp authored on 16/02/2011 15:57:42
Viewb027096

clean up shrinkSummary (chr.x is no longer needed)

Rob Scharp authored on 16/02/2011 15:57:39