Changes between Version 8 and Version 9 of GwasQcPipeline

Timestamp:

Feb 10, 2011 5:35:13 PM (14 years ago)

Author:

Morris Swertz

Comment:

--

GwasQcPipeline

@@ -36 +36 @@
 Get missing data information:
 
- {{{p-link --bfile GvNL_raw_final --missing --out GvNL_raw_final}}}
+{{{p-link --bfile GvNL_raw_final --missing --out GvNL_raw_final}}}
  
 Get heterozygocity information: 
@@ -45 +45 @@
 * In R: 
 
-{{{het <- read.table("GvNL_raw_final.het", head=TRUE)&#10;mis <- read.table("GvNL_raw_final.imiss", head=TRUE)&#10;het$HET_RATE = (het$"N.NM." - het$"O.HOM.")/het$"N.NM."&#10;plot (mis$F_MISS,het$HET_RATE, xlab="Missing SNPs", ylab="Heterozygocity Rate")}}}
+{{{
+het <- read.table("GvNL_raw_final.het", head=TRUE)
+mis <- read.table("GvNL_raw_final.imiss", head=TRUE);
+het$HET_RATE = (het$"N.NM." - het$"O.HOM.")/het$"N.NM."&#10;plot (mis$F_MISS,het$HET_RATE, xlab="Missing SNPs", ylab="Heterozygocity Rate")}}}
 
 No samples with callrate < 95% (Filtered in lab)
@@ -53 +56 @@
 In R: 
 
-{{{het_fail = subset(het, (het$HET_RATE < mean(het$HET_RATE)-3*sd(het$HET_RATE)) | (het$HET_RATE > mean(het$HET_RATE)+3*sd(het$HET_RATE)))&#10;het_fail$HET_DST = (het_fail$HET_RATE-mean(het$HET_RATE))/sd(het$HET_RATE)&#10;write.table(het_fail, "fail-het-qc.txt", row.names=FALSE)}}}
+{{{
+het_fail = subset(het, (het$HET_RATE < mean(het$HET_RATE)-3*sd(het$HET_RATE)) | (het$HET_RATE > mean(het$HET_RATE)+3*sd(het$HET_RATE)));
+het_fail$HET_DST = (het_fail$HET_RATE-mean(het$HET_RATE))/sd(het$HET_RATE);
+write.table(het_fail, "fail-het-qc.txt", row.names=FALSE)}}}
 
 Result: