| ... | ... |
@@ -556,3 +556,6 @@ function (which expects ff objects and supports parallel processing) |
| 556 | 556 |
** added functions get.ProtocolData.Illumina(), construct.Illumina() and genotype.Illumina() to maintiain consistency with Rob's Affy functions |
| 557 | 557 |
** removed 'save.it', 'load.it', 'snpFile', 'cnFile' arguments from crlmmIllumina(), crlmmIlluminaV2 and preprocessInfinium2(). Updated man pages to reflect these changes. |
| 558 | 558 |
** added a switch so that both regular matrix/ff storage can be handled in each function, depending upon whether the ff package has been loaded. |
| 559 |
+ |
|
| 560 |
+2010-09-30 M. Ritchie 1.7.16 |
|
| 561 |
+** copy number A and B intensities now stored in callSet from genotype.Illumina() |
| ... | ... |
@@ -1,8 +1,8 @@ |
| 1 | 1 |
Package: crlmm |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays. |
| 4 |
-Version: 1.7.15 |
|
| 5 |
-Date: 2010-09-27 |
|
| 4 |
+Version: 1.7.16 |
|
| 5 |
+Date: 2010-09-30 |
|
| 6 | 6 |
Author: Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry |
| 7 | 7 |
Maintainer: Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU> |
| 8 | 8 |
Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms |
| ... | ... |
@@ -1292,6 +1292,7 @@ genotype.Illumina <- function(sampleSheet=NULL, |
| 1292 | 1292 |
# save.it=save.it, snpFile=snpFile, cnFile=cnFile) |
| 1293 | 1293 |
rm(XY); gc() |
| 1294 | 1294 |
if(verbose) message("Finished preprocessing.")
|
| 1295 |
+ np.index <- which(!is.snp) |
|
| 1295 | 1296 |
if(is.lds){
|
| 1296 | 1297 |
open(res[["A"]]) |
| 1297 | 1298 |
open(res[["B"]]) |
| ... | ... |
@@ -1300,14 +1301,27 @@ genotype.Illumina <- function(sampleSheet=NULL, |
| 1300 | 1301 |
bb = ocProbesets()*ncol(A)*8 |
| 1301 | 1302 |
ffrowapply(A(callSet)[i1:i2, ] <- res[["A"]][i1:i2, ], X=res[["A"]], BATCHBYTES=bb) |
| 1302 | 1303 |
ffrowapply(B(callSet)[i1:i2, ] <- res[["B"]][i1:i2, ], X=res[["B"]], BATCHBYTES=bb) |
| 1304 |
+ if(length(np.index)>0) {
|
|
| 1305 |
+ for (j in 1:ncol(callSet)) {
|
|
| 1306 |
+ A(callSet)[np.index, j] <- res[["cnAB"]]$A[,j] |
|
| 1307 |
+ B(callSet)[np.index, j] <- res[["cnAB"]]$B[,j] |
|
| 1308 |
+ } |
|
| 1309 |
+ } |
|
| 1310 |
+ |
|
| 1303 | 1311 |
} else{
|
| 1304 | 1312 |
A(callSet)[snp.index, ] <- res[["A"]] |
| 1305 | 1313 |
B(callSet)[snp.index, ] <- res[["B"]] |
| 1314 |
+ if(length(np.index)>0) {
|
|
| 1315 |
+ for (j in 1:ncol(callSet)) {
|
|
| 1316 |
+ A(callSet)[np.index, ] <- res[["cnAB"]]$A |
|
| 1317 |
+ B(callSet)[np.index, ] <- res[["cnAB"]]$B |
|
| 1318 |
+ } |
|
| 1319 |
+ } |
|
| 1306 | 1320 |
} |
| 1307 | 1321 |
pData(callSet)$SKW <- res[["SKW"]] |
| 1308 | 1322 |
pData(callSet)$SNR <- res[["SNR"]] |
| 1309 | 1323 |
mixtureParams <- res[["mixtureParams"]] |
| 1310 |
-# np.index <- which(!is.snp) |
|
| 1324 |
+ |
|
| 1311 | 1325 |
# if(verbose) message("Normalizing nonpolymorphic markers")
|
| 1312 | 1326 |
# FUN <- ifelse(is.lds, "cnrma2", "cnrma") |
| 1313 | 1327 |
## main purpose is to update 'alleleA' |
