### R code from vignette source 'nuCpos-intro.Rnw'

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### code chunk number 1: nuCpos-intro.Rnw:89-90
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library(nuCpos)


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### code chunk number 2: nuCpos-intro.Rnw:106-109
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predNuCpos(file = system.file("extdata", "TRP1ARS1x1.fasta", 
    package = "nuCpos"), species = "sc", smoothHBA = FALSE, 
    ActLikePredNuPoP = TRUE)


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### code chunk number 3: nuCpos-intro.Rnw:135-139
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library(NuPoP)
results.TRP1ARS1x1 <- readNuPoP("TRP1ARS1x1.fasta_Prediction4.txt", 
    startPos = 1, endPos = 1465)
results.TRP1ARS1x1[1:5,]


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### code chunk number 4: nuCpos-intro.Rnw:149-150
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results.TRP1ARS1x1[72:76,]


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### code chunk number 5: nuCpos-intro.Rnw:161-162
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plotNuPoP(results.TRP1ARS1x1)


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### code chunk number 6: nuCpos-intro.Rnw:171-176
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predNuCpos(file = system.file("extdata", "TRP1ARS1x3.fasta", 
    package = "nuCpos"), species = "sc", smoothHBA = FALSE, 
    ActLikePredNuPoP = TRUE)
results.TRP1ARS1 <- readNuPoP("TRP1ARS1x3.fasta_Prediction4.txt", 
    startPos = 1466, endPos = 2930)


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### code chunk number 7: nuCpos-intro.Rnw:186-202
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par(mfrow = c(2, 1))
plot(x = 1:1465, y = results.TRP1ARS1x1[,3], type = "n", 
    ylim = c(-0.05, 1), xlab = "Position from the EcoRI site #1", 
    ylab = "probability/occupancy")
title("Not triplicated")
polygon(c(1, 1:1465, 1465), c(0, results.TRP1ARS1x1[,3], 0), col = 8)
points(x = 1:1465, y = results.TRP1ARS1x1[,4], type = "l", col = 2)
points(x = 1:1465, y = results.TRP1ARS1x1[, 2], type = "h", col = 4)

plot(x = 1:1465, y = results.TRP1ARS1[,3], type = "n", 
    ylim = c(-0.05, 1), xlab = "Position from the EcoRI site #1", 
    ylab = "probability/occupancy")
title("Triplicated: central copy")
polygon(c(1, 1:1465, 1465), c(0, results.TRP1ARS1[,3], 0), col = 8)
points(x = 1:1465, y = results.TRP1ARS1[,4], type = "l", col = 2)
points(x = 1:1465, y = results.TRP1ARS1[, 2], type = "h", col = 4)


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### code chunk number 8: nuCpos-intro.Rnw:210-230
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predNuCpos(file = system.file("extdata", "TRP1ARS1x3.fasta", 
    package = "nuCpos"), species = "sc", smoothHBA = TRUE, 
    ActLikePredNuPoP = TRUE)
results.TRP1ARS1.smooth <- readNuPoP("TRP1ARS1x3.fasta_Prediction4.txt", 
    startPos = 1466, endPos = 2930)

par(mfrow = c(2, 1))
plot(x = 1:1465, y = results.TRP1ARS1[,3], type = "n", 
    ylim = c(-0.05, 1), xlab = "Position from the EcoRI site #1", 
    ylab = "probability/occupancy")
title("Occupancy(grey)/probability(blue)/Viterbi(red)")
polygon(c(1, 1:1465, 1465), c(0, results.TRP1ARS1[,3], 0), col = 8)
points(x = 1:1465, y = results.TRP1ARS1[,4], type = "l", col = 2)
points(x = 1:1465, y = results.TRP1ARS1[, 2], type = "h", col = 4)

plot(x = 1:1465, y = results.TRP1ARS1[,5], type = "n", 
    xlab = "Position from the EcoRI site #1", 
    ylab = "HBA", main = "HBA(red)/smoothed HBA(blue)")
points(x = 1:1465, y = results.TRP1ARS1[,5], type = "l", col = 2)
points(x = 1:1465, y = results.TRP1ARS1.smooth[,5], type = "l", col = 4)


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### code chunk number 9: nuCpos-intro.Rnw:261-268
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TRP1ARS1 <- paste(scan(file = 
    system.file("extdata", "TRP1ARS1x1.fasta", package = "nuCpos"), 
    what = character(), skip = 1), sep = "", collapse = "")
results.TRP1ARS1.internal <- 
    predNuCpos(inseq = TRP1ARS1, species = "sc", smoothHBA = FALSE, 
    ActLikePredNuPoP = FALSE)
results.TRP1ARS1.internal[72:76,]


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### code chunk number 10: nuCpos-intro.Rnw:280-288
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load(system.file("extdata", "inseq.RData", package = "nuCpos"))
HBA(inseq = inseq, species = "sc")
for(i in 1:3) cat(substr(inseq, start = (i-1)*60+1, 
    stop = (i-1)*60+60), "\n")
load(system.file("extdata", "INSEQ_DNAString.RData", 
    package = "nuCpos"))
INSEQ
HBA(inseq = INSEQ, species = "sc")


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### code chunk number 11: nuCpos-intro.Rnw:316-320
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localHBA(inseq = inseq, species = "sc")
barplot(localHBA(inseq = inseq, species = "sc"), 
    names.arg = LETTERS[1:13], xlab = "Nucleosomal subsegments", 
    ylab = "local HBA", main = "Local HBA scores for inseq")