Browse code

increased indentation of verbose output for probe stratum

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52816 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 15:57:09
Showing1 changed files

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@@ -319,7 +319,7 @@ fit.wls <- function(NN, sigma, allele, Y, autosome, X){
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 shrinkGenotypeSummaries <- function(strata, index.list, object, MIN.OBS, MIN.SAMPLES, DF.PRIOR,
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 				    verbose, is.lds){
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 	if(is.lds) {physical <- get("physical"); open(object)}
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-	if(verbose) message("Probe stratum ", strata, " of ", length(index.list))
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+	if(verbose) message("      Probe stratum ", strata, " of ", length(index.list))
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 	marker.index <- index.list[[strata]]
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 	batches <- split(seq_along(batch(object)), as.character(batch(object)))
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 	batches <- batches[sapply(batches, length) >= MIN.SAMPLES]
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@@ -455,7 +455,7 @@ fit.lm1 <- function(strata,
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 		    verbose, is.lds,
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 		    CHR.X, ...){
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 	if(is.lds) {physical <- get("physical"); open(object)}
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-	if(verbose) message("Probe stratum ", strata, " of ", length(index.list))
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+	if(verbose) message("      Probe stratum ", strata, " of ", length(index.list))
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 	snps <- index.list[[strata]]
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 	batches <- split(seq_along(batch(object)), as.character(batch(object)))
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 	batches <- batches[sapply(batches, length) >= MIN.SAMPLES]
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@@ -535,7 +535,7 @@ fit.lm2 <- function(strata,
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 		    MIN.PHI,
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 		    verbose, is.lds, CHR.X, ...){
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 	if(is.lds) {physical <- get("physical"); open(object)}
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-	if(verbose) message("Probe stratum ", strata, " of ", length(index.list))
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+	if(verbose) message("      Probe stratum ", strata, " of ", length(index.list))
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 	marker.index <- index.list[[strata]]
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 	batches <- split(seq_along(batch(object)), as.character(batch(object)))
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 	batches <- batches[sapply(batches, length) >= MIN.SAMPLES]
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@@ -717,7 +717,7 @@ fit.lm3 <- function(strata,
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 		    MIN.PHI,
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 		    verbose, is.lds, CHR.X, ...){
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 	if(is.lds) {physical <- get("physical"); open(object)}
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-	if(verbose) message("Probe stratum ", strata, " of ", length(index.list))
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+	if(verbose) message("      Probe stratum ", strata, " of ", length(index.list))
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 	gender <- object$gender
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 	enough.males <- sum(gender==1) > MIN.SAMPLES
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 	enough.females <- sum(gender==2) > MIN.SAMPLES
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@@ -879,7 +879,7 @@ fit.lm4 <- function(strata,
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 		message(paste("fewer than", MIN.SAMPLES, "men and women.  Copy number not estimated for CHR X"))
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 		return(object)
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 	}
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-	if(verbose) message("Probe stratum ", strata, " of ", length(index.list))
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+	if(verbose) message("      Probe stratum ", strata, " of ", length(index.list))
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 	marker.index <- index.list[[strata]]
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 	batches <- split(seq_along(batch(object)), as.character(batch(object)))
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 	batches <- batches[sapply(batches, length) >= MIN.SAMPLES]
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@@ -1396,7 +1396,7 @@ whichMarkers <- function(type, is.snp, is.autosome, is.annotated, is.X){
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 summarizeNps <- function(strata, index.list, object, batchSize,
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 			 GT.CONF.THR, verbose, is.lds, CHR.X, ...){
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 	if(is.lds) {physical <- get("physical"); open(object)}
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-	if(verbose) message("Probe stratum ", strata, " of ", length(index.list))
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+	if(verbose) message("      Probe stratum ", strata, " of ", length(index.list))
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 	index <- index.list[[strata]]
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 	if(CHR.X) {
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 		sample.index <- which(object$gender==2)
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@@ -1449,7 +1449,7 @@ summarizeSnps <- function(strata,
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 		physical <- get("physical")
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 		open(object)
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 	}
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-	if(verbose) message("Probe stratum ", strata, " of ", length(index.list))
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+	if(verbose) message("      Probe stratum ", strata, " of ", length(index.list))
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 	index <- index.list[[strata]]
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 ##	if(CHR.X) {
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 ##		sample.index <- which(object$gender==2)