[Genabel-commits] r624 - pkg/GenABEL/R

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

Author: maksim
Date: 2010-12-17 00:06:08 +0100 (Fri, 17 Dec 2010)
New Revision: 624

Modified:
   pkg/GenABEL/R/merge.snp.data.R
Log:
The additional info in error output added for merge.snp.data function. If there is any difference in chromosome names for intersected SNPs then the output file is generated where position of worong snps are saved.

Modified: pkg/GenABEL/R/merge.snp.data.R
===================================================================
--- pkg/GenABEL/R/merge.snp.data.R	2010-12-07 21:42:43 UTC (rev 623)
+++ pkg/GenABEL/R/merge.snp.data.R	2010-12-16 23:06:08 UTC (rev 624)
@@ -129,10 +129,27 @@
 
 
 chromosome_logic_vec <- c(as.character(x at chromosome[which_snp_intersect_in_x])) == c(as.character(y at chromosome[which_snp_intersect_in_y]))
-chromosome_logic_vec <- factor(chromosome_logic_vec)
-if(length(levels(chromosome_logic_vec)) > 1) stop("For intersected SNPs several values in chromosome vector for x is not concur with values in y. Check your data sets.\n") 
+chromosome_logic_vec_factor <- factor(chromosome_logic_vec)
+if(length(levels(chromosome_logic_vec_factor)) > 1)
+	{
+	position_of_error_snps_in_x <- which_snp_intersect_in_x[!chromosome_logic_vec]
+	position_of_error_snps_in_y <- which_snp_intersect_in_y[!chromosome_logic_vec]
+	
+	error_output <- data.frame(snp_positon_in_x=position_of_error_snps_in_x, 
+														 snp_positon_in_y=position_of_error_snps_in_y, 
+														 snpname_in_x=x at snpnames[position_of_error_snps_in_x],
+														 snpname_in_y=y at snpnames[position_of_error_snps_in_y],
+														 chromosome_in_x=as.character(x at chromosome)[position_of_error_snps_in_x],
+														 chromosome_in_y=as.character(y at chromosome)[position_of_error_snps_in_y],
+														 codding_in_x=as.character(x at coding[position_of_error_snps_in_x]),
+														 codding_in_y=as.character(y at coding[position_of_error_snps_in_y]))
+	write.table(error_output, file="merge_snp_data_chromosome_error.txt", row.names=F, quote=F)	
+	non_overlaped_chr_num <- table(chromosome_logic_vec)[1]
+	stop(paste("There is difference found in chromosome names for ", non_overlaped_chr_num," intersected SNPs. It is expected that all snps have exactly the same names of chromosome. Capital/lower-case letters are considered as different. The file merge_snp_data_chromosome_error.txt contains information about the SNPs having wrong chromosome number. The column snp_positon_in_x and snp_positon_in_y contains order position in x (first) and y (second) input data set. Check column chromosome_in_x and chromosome_in_y and replace the chromosome names in input data set.\n"), sep="") 
+#	stop("For intersected SNPs several values in chromosome vector for x is not concur with values in y. Check your data sets.\n") 
+	}
 
-if(length(levels(chromosome_logic_vec)) == 0)
+if(length(levels(chromosome_logic_vec_factor)) == 0)
 	{
 	cat("There are not intersected SNPs\n")
 	}