[Genabel-commits] r1174 - pkg/GenABEL/R

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2013-03-25 00:52:58 +0100 (Mon, 25 Mar 2013)
New Revision: 1174

Modified:
   pkg/GenABEL/R/ccfast.R
   pkg/GenABEL/R/ccfast.new.R
   pkg/GenABEL/R/load.gwaa.data.R
   pkg/GenABEL/R/qtscore.R
   pkg/GenABEL/R/snp.names.R
Log:
Fixed a minor spelling error in a few GenABEL files

Modified: pkg/GenABEL/R/ccfast.R
===================================================================
--- pkg/GenABEL/R/ccfast.R	2013-03-24 23:41:49 UTC (rev 1173)
+++ pkg/GenABEL/R/ccfast.R	2013-03-24 23:52:58 UTC (rev 1174)
@@ -14,7 +14,7 @@
 	cc <- phdata(data)[[y]]
 
         if (length(levels(as.factor(cc)))<2) stop("cc status is monomorphic!") 
-        if (length(levels(as.factor(cc)))>2) stop("cc status has more then 2 levels!") 
+        if (length(levels(as.factor(cc)))>2) stop("cc status has more than 2 levels!") 
         if (levels(as.factor(cc))[1] != 0 || levels(as.factor(cc))[2] != 1) stop ("cc is case-control status, with 0 as control and 1 as cases. No 0 and/or 1 found in the data")
 
 	if (any(is.na(cc))) {

Modified: pkg/GenABEL/R/ccfast.new.R
===================================================================
--- pkg/GenABEL/R/ccfast.new.R	2013-03-24 23:41:49 UTC (rev 1173)
+++ pkg/GenABEL/R/ccfast.new.R	2013-03-24 23:52:58 UTC (rev 1174)
@@ -14,7 +14,7 @@
 	cc <- phdata(data)[[y]]
 
         if (length(levels(as.factor(cc)))<2) stop("cc status is monomorphic!") 
-        if (length(levels(as.factor(cc)))>2) stop("cc status has more then 2 levels!") 
+        if (length(levels(as.factor(cc)))>2) stop("cc status has more than 2 levels!") 
         if (levels(as.factor(cc))[1] != 0 || levels(as.factor(cc))[2] != 1) stop ("cc is case-control status, with 0 as control and 1 as cases. No 0 and/or 1 found in the data")
 
 	if (any(is.na(cc))) {

Modified: pkg/GenABEL/R/load.gwaa.data.R
===================================================================
--- pkg/GenABEL/R/load.gwaa.data.R	2013-03-24 23:41:49 UTC (rev 1173)
+++ pkg/GenABEL/R/load.gwaa.data.R	2013-03-24 23:52:58 UTC (rev 1174)
@@ -19,7 +19,7 @@
 	}
 ####
 	if (length(a) > 2)
-		stop("column named \"sex\" contains more then 2 codes")
+		stop("column named \"sex\" contains more than 2 codes")
 	if (length(a) == 1 && !(names(a)[1] == 0 || names(a)[1] == 1))
 		stop("the column named \"sex\" contains 1 code which is neither 0 (=female) or 1 (=male)")
 	if (length(a) == 2 && names(a)[1] != 0 && names(a)[2] != 1)

Modified: pkg/GenABEL/R/qtscore.R
===================================================================
--- pkg/GenABEL/R/qtscore.R	2013-03-24 23:41:49 UTC (rev 1173)
+++ pkg/GenABEL/R/qtscore.R	2013-03-24 23:52:58 UTC (rev 1174)
@@ -30,7 +30,7 @@
 #' @param strata Stratification variable. If provieded, scores are computed within strata and 
 #' then added up.
 #' @param trait.type "gaussian" or "binomial" or "guess" (later option guesses trait type)
-#' @param times If more then one, the number of replicas to be used in derivation of 
+#' @param times If more than one, the number of replicas to be used in derivation of 
 #' empirical genome-wide significance. See \code{\link{emp.qtscore}}, which
 #' calls qtscore with times>1 for details
 #' @param quiet do not print warning messages

Modified: pkg/GenABEL/R/snp.names.R
===================================================================
--- pkg/GenABEL/R/snp.names.R	2013-03-24 23:41:49 UTC (rev 1173)
+++ pkg/GenABEL/R/snp.names.R	2013-03-24 23:52:58 UTC (rev 1174)
@@ -72,7 +72,7 @@
 		if (length(end)>1) stop("end must be single number!")
 		if (end < min(data at map)) return(NULL)
 	}
-	if (begin > end) stop("Start-map parameter begin must be more then end-parameter")
+	if (begin > end) stop("Start-map parameter begin must be more than end-parameter")
 	data <- data[,data at snpnames[data at map>=begin & data at map<=end]]
 	out <- data at snpnames
 	out