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comparison report_clonality/RScript.r @ 1:90a05ff900db draft

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author davidvanzessen
date Mon, 05 Sep 2016 04:46:06 -0400
parents afe85eb6572e
children beaa487ecf43
comparison
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0:afe85eb6572e 1:90a05ff900db
112 #again for clonalityFrame but with sample+replicate 112 #again for clonalityFrame but with sample+replicate
113 clonalityFrame$clonaltype = do.call(paste, c(clonalityFrame[unlist(strsplit(clonaltype, ","))], sep = ":")) 113 clonalityFrame$clonaltype = do.call(paste, c(clonalityFrame[unlist(strsplit(clonaltype, ","))], sep = ":"))
114 clonalityFrame$clonality_clonaltype = do.call(paste, c(clonalityFrame[unlist(strsplit(paste(clonaltype, ",Replicate", sep=""), ","))], sep = ":")) 114 clonalityFrame$clonality_clonaltype = do.call(paste, c(clonalityFrame[unlist(strsplit(paste(clonaltype, ",Replicate", sep=""), ","))], sep = ":"))
115 clonalityFrame = clonalityFrame[!duplicated(clonalityFrame$clonality_clonaltype), ] 115 clonalityFrame = clonalityFrame[!duplicated(clonalityFrame$clonality_clonaltype), ]
116 } 116 }
117
118 print("SAMPLE TABLE:")
119 print(table(PRODF$Sample))
117 120
118 prod.unique.sample.count = data.frame(data.table(PRODF)[, list(Productive_unique=.N), by=c("Sample")]) 121 prod.unique.sample.count = data.frame(data.table(PRODF)[, list(Productive_unique=.N), by=c("Sample")])
119 prod.unique.rep.count = data.frame(data.table(PRODF)[, list(Productive_unique=.N), by=c("Sample", "Replicate")]) 122 prod.unique.rep.count = data.frame(data.table(PRODF)[, list(Productive_unique=.N), by=c("Sample", "Replicate")])
120 123
121 unprod.unique.sample.count = data.frame(data.table(UNPROD)[, list(Unproductive_unique=.N), by=c("Sample")]) 124 unprod.unique.sample.count = data.frame(data.table(UNPROD)[, list(Unproductive_unique=.N), by=c("Sample")])