[Genabel-commits] r1896 - pkg/MultiABEL/R

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

Author: shenxia
Date: 2014-12-05 12:28:54 +0100 (Fri, 05 Dec 2014)
New Revision: 1896

Modified:
   pkg/MultiABEL/R/MultiMeta.R
   pkg/MultiABEL/R/MultiRep.R
   pkg/MultiABEL/R/Multivariate.R
Log:
v. 1.0-2; lines shortened; curly brackets added around "if" - "else" body; phdata() used instead of @phdata for stability.

Modified: pkg/MultiABEL/R/MultiMeta.R
===================================================================
--- pkg/MultiABEL/R/MultiMeta.R	2014-12-02 08:12:52 UTC (rev 1895)
+++ pkg/MultiABEL/R/MultiMeta.R	2014-12-05 11:28:54 UTC (rev 1896)
@@ -50,7 +50,9 @@
         }
         common <- common[common %in% rownames(reslist[[i]])]
     }
-    if (length(common) == 0) stop('no variant exists in all studies!')
+    if (length(common) == 0) {
+		stop('no variant exists in all studies!')
+	}
     cat(' OK\n')
     cat('meta-analysis ...')
     pmat <- matrix(NA, length(common), k + 1)

Modified: pkg/MultiABEL/R/MultiRep.R
===================================================================
--- pkg/MultiABEL/R/MultiRep.R	2014-12-02 08:12:52 UTC (rev 1895)
+++ pkg/MultiABEL/R/MultiRep.R	2014-12-05 11:28:54 UTC (rev 1896)
@@ -103,7 +103,9 @@
     cat(' OK\n')
     if (ncol(training.geno) != 1) {
         cat('replication analysis ...\n')
-    } else cat('replication analysis ...')
+    } else {
+		cat('replication analysis ...')
+	}
     for (k in 1:ncol(training.geno)) {
         m0 <- lm(training.geno[,k] ~ Y0)
         training.coef[,k] <- m0$coef[-1]
@@ -112,8 +114,14 @@
         cy <- Y1 %*% training.coef[,k]
         mrep <- lm(cy ~ test.geno[,k])
         reptab[k,] <- c(summary(mrep)$coef[2,c(1:2, 4)], summary(mrep)$r.squared)
-        if (ncol(training.geno) != 1) progress(k/ncol(training.geno)*100)
+        if (ncol(training.geno) != 1) {
+			progress(k/ncol(training.geno)*100)
+		}
     }
-    if (ncol(training.geno) == 1) cat(' OK\n') else cat('\n')
+    if (ncol(training.geno) == 1) {
+		cat(' OK\n')
+	} else {
+		cat('\n')
+	}
     return(list(replication = reptab, training.coef = training.coef, test.coef = test.coef))
 }

Modified: pkg/MultiABEL/R/Multivariate.R
===================================================================
--- pkg/MultiABEL/R/Multivariate.R	2014-12-02 08:12:52 UTC (rev 1895)
+++ pkg/MultiABEL/R/Multivariate.R	2014-12-05 11:28:54 UTC (rev 1896)
@@ -60,28 +60,50 @@
 `Multivariate` <- function(gwaa.data = NULL, phenofile = NULL, genofile = NULL, outfile = 'Multivariate_GWAS_results.txt', 
                            trait.cols, covariate.cols = NULL, cuts = 20, ...) {
     cat('loading data ...')
-    if (length(trait.cols) == 1) stop('select multiple traits to analyze!')
+    if (length(trait.cols) == 1) {
+		stop('select multiple traits to analyze!')
+	}
     if (!is.null(phenofile) & !is.null(genofile)) {
         pheno <- read.table(phenofile, header = TRUE)
         geno <- databel(genofile)
-        if (nrow(pheno) != nrow(geno)) stop('sizes of phenofile and genofile do not match!')
+        if (nrow(pheno) != nrow(geno)) {
+			stop('sizes of phenofile and genofile do not match!')
+		}
         GenABEL <- FALSE
         cat(' OK\n')
     } else if (!is.null(gwaa.data)) {
-        if (!is.null(phenofile)) pheno <- read.table(phenofile, header = TRUE) else pheno <- gwaa.data at phdata
+        if (!is.null(phenofile)) {
+			pheno <- read.table(phenofile, header = TRUE)
+		} else {
+			pheno <- phdata(gwaa.data)
+		}
         GenABEL <- TRUE
         cat(' OK\n')
     } else {
         stop('insufficient data input!')
     }
     cat('initializing analysis ...')
-    if (!GenABEL) res <- matrix(NA, ncol(geno), 5) else res <- matrix(NA, ncol(gwaa.data at gtdata), 5)
+    if (!GenABEL) {
+		res <- matrix(NA, ncol(geno), 5)
+	} else {
+		res <- matrix(NA, ncol(gwaa.data at gtdata), 5)
+	}
     colnames(res) <- c('MANOVA.stat', 'F.stat', 'df.num', 'df.den', 'P.F')
-    if (!GenABEL) rownames(res) <- colnames(geno) else rownames(res) <- gwaa.data at gtdata@snpnames
+    if (!GenABEL) {
+		rownames(res) <- colnames(geno)
+	} else {
+		rownames(res) <- gwaa.data at gtdata@snpnames
+	}
     Y <- as.matrix(pheno[,trait.cols]) 
     X <- matrix(1, nrow(Y), 1)
-    if (!is.null(covariate.cols)) X <- cbind(X, as.matrix(pheno[,covariate.cols]))
-    if (!GenABEL) nsnp <- ncol(geno) else nsnp <- ncol(gwaa.data at gtdata)
+    if (!is.null(covariate.cols)) {
+		X <- cbind(X, as.matrix(pheno[,covariate.cols]))
+	}
+    if (!GenABEL) {
+		nsnp <- ncol(geno)
+	} else {
+		nsnp <- ncol(gwaa.data at gtdata)
+	}
     if (cuts != 1) {
         cutpoints <- round(seq(1, nsnp, length = cuts + 1)) 
         starts <- cutpoints[1:cuts]
@@ -93,17 +115,31 @@
     cat(' OK\n')
     if (cuts != 1) {
         cat('multivariate GWA scan ...\n')
-    } else cat('multivariate GWA scan ...')
+    } else {
+		cat('multivariate GWA scan ...')
+	}
     for (k in 1:cuts) {
         idx <- starts[k]:ends[k]
-        if (!GenABEL) g <- databel2matrix(geno[,idx]) else g <- as.double(gwaa.data at gtdata[,idx])
+        if (!GenABEL) {
+			g <- databel2matrix(geno[,idx])
+		} else {
+			g <- as.double(gwaa.data at gtdata[,idx])
+		}
         for (j in 1:ncol(g)) {
             stats <- try(summary(manova(Y ~ 0 + X + g[,j]), ...)$stats, silent = TRUE)
-            if (!inherits(stats, 'try-error')) res[idx[j],] <- stats[nrow(stats) - 1,-1]
+            if (!inherits(stats, 'try-error')) {
+				res[idx[j],] <- stats[nrow(stats) - 1,-1]
+			}
         }
-        if (cuts != 1) progress(k/cuts*100)
+        if (cuts != 1) {
+			progress(k/cuts*100)
+		}
     }
-    if (cuts == 1) cat(' OK\n') else cat('\n')
+    if (cuts == 1) {
+		cat(' OK\n')
+	} else {
+		cat('\n')
+	}
     cat('writing results ...')
     write.table(res, outfile, row.names = TRUE, col.names = TRUE, quote = FALSE, sep = '\t')
     cat(' OK\n')