should not use snp.index when retrieving the centers. Replace with seq_len(nrow(cnSet))
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58759 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 04/10/2011 16:11:40
| ... | ... |
@@ -2766,7 +2766,8 @@ ABpanel <- function(x, y, predictRegion, |
| 2766 | 2766 |
calculateRTheta <- function(cnSet, genotype=c("AA", "AB", "BB"), batch.name){
|
| 2767 | 2767 |
genotype <- match.arg(genotype) |
| 2768 | 2768 |
j <- match(batch.name, batchNames(cnSet)) |
| 2769 |
- centers <- medians(cnSet, i=snp.index, j) |
|
| 2769 |
+ ##centers <- medians(cnSet, i=snp.index, j) |
|
| 2770 |
+ centers <- medians(cnSet, i=seq_len(nrow(cnSet)), j) |
|
| 2770 | 2771 |
theta <- matrix(NA, nrow(cnSet), 2) |
| 2771 | 2772 |
colnames(theta) <- c("theta", "R")
|
| 2772 | 2773 |
x <- centers[, "A", genotype, 1] |