Mercurial > repos > rhpvorderman > shm_csr

annotate change_o/define_clones.r @ 5:495a521cf9f2 draft

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"planemo upload commit 40d62ec3d2fea3c3bac605c976941e1f3b7e2cd4"
author rhpvorderman
date Tue, 16 Nov 2021 11:16:06 +0000
parents 64d74ba01a7c
children
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64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
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1 args <- commandArgs(trailingOnly = TRUE)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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3 input=args[1]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
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4 output=args[2]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
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6 change.o = read.table(input, header=T, sep="\t", quote="", stringsAsFactors=F)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
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8 freq = data.frame(table(change.o$CLONE))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
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9 freq2 = data.frame(table(freq$Freq))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
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11 freq2$final = as.numeric(freq2$Freq) * as.numeric(as.character(freq2$Var1))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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13 names(freq2) = c("Clone size", "Nr of clones", "Nr of sequences")
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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15 write.table(x=freq2, file=output, sep="\t",quote=F,row.names=F,col.names=T)