17 lines
632 B
R
17 lines
632 B
R
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## need seqz file and sample name
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args=commandArgs(T)
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sample=args[1]
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seqz=args[2]
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out_prefix=args[3]
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library("sequenza")
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Sys.setenv("VROOM_CONNECTION_SIZE" = 131072 * 1000)
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#seqz.data <- read.seqz(CCW0032_small.seqz.gz)
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#gc.stats <- gc.norm(x = seqz.data$depth.ratio,gc = seqz.data$GC.percent)
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#gc.vect <- setNames(gc.stats$raw.mean, gc.stats$gc.values)
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#seqz.data$adjusted.ratio <- seqz.data$depth.ratio/gc.vect[as.character(seqz.data$GC.percent)]
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test <- sequenza.extract(args[2])
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#names(test)
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CP.example <- sequenza.fit(test)
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sequenza.results(sequenza.extract = test, cp.table = CP.example,sample.id = args[1], out.dir=args[3])
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