SNPs on chr X are summarized during fit.lm3 through the call to summarizeXGenotypes
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52820 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 16/02/2011 15:57:24 | ... | ... |
@@ -1392,7 +1392,7 @@ genotypeSummary <- function(object, |
| 1392 | 1392 |
switch(type, |
| 1393 | 1393 |
SNP="summarizeSnps", |
| 1394 | 1394 |
NP="summarizeNps", |
| 1395 |
- X.SNP="summarizeSnps", |
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+## X.SNP="summarizeSnps", |
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| 1396 | 1396 |
X.NP="summarizeNps") |
| 1397 | 1397 |
} |
| 1398 | 1398 |
myf <- summaryFxn(type[[1]]) |
| ... | ... |
@@ -1650,12 +1650,9 @@ crlmmCopynumber <- function(object, |
| 1650 | 1650 |
X.SNP="chromosome X SNPs", |
| 1651 | 1651 |
X.NP="chromosome X nonpolymorphic markers") |
| 1652 | 1652 |
} |
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- if(verbose & is.lds) {
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- message("Large data support with ff package is enabled.")
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| 1655 |
- message("To reduce RAM, the markers are divided into several strata (see ?ocProbesets for details) and summary statistics are computed on each stratum")
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| 1656 |
- } |
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| 1657 |
- for(i in seq_along(type)){
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- ## do all types |
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+ if(verbose) message("Computing summary statistics of the genotype clusters for each batch")
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+## for(i in seq_along(type)){
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+ for(i in c(1, 2, 4)){ ## do not do X.SNP. Do this during fit.lm3
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| 1659 | 1656 |
marker.type <- type[i] |
| 1660 | 1657 |
if(verbose) message(paste("...", mylabel(marker.type)))
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| 1661 | 1658 |
##if(verbose) message(paste("Computing summary statistics for ", mylabel(marker.type), " genotype clusters for each batch")
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