### R code from vignette source 'nuCpos-intro.Rnw' ################################################### ### code chunk number 1: nuCpos-intro.Rnw:82-83 ################################################### library(nuCpos) ################################################### ### code chunk number 2: nuCpos-intro.Rnw:99-102 ################################################### predNuCpos(file = system.file("extdata", "TRP1ARS1x1.fasta", package = "nuCpos"), species = "sc", smoothHBA = FALSE, ActLikePredNuPoP = TRUE) ################################################### ### code chunk number 3: nuCpos-intro.Rnw:128-132 ################################################### library(NuPoP) results.TRP1ARS1x1 <- readNuPoP("TRP1ARS1x1.fasta_Prediction4.txt", startPos = 1, endPos = 1465) results.TRP1ARS1x1[1:5,] ################################################### ### code chunk number 4: nuCpos-intro.Rnw:142-143 ################################################### results.TRP1ARS1x1[72:76,] ################################################### ### code chunk number 5: nuCpos-intro.Rnw:154-155 ################################################### plotNuPoP(results.TRP1ARS1x1) ################################################### ### code chunk number 6: nuCpos-intro.Rnw:164-169 ################################################### 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) ################################################### ### code chunk number 7: nuCpos-intro.Rnw:179-195 ################################################### 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) ################################################### ### code chunk number 8: nuCpos-intro.Rnw:211-233 ################################################### predNuPoP(file = system.file("extdata", "TRP1ARS1x3.fasta", package = "nuCpos"), species = 7, model = 4) results.NuPoP <- 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("NuCpos: Eight nucleosomes on the Viterbi path") 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) text(x = 800, y = 0.5, labels = "*", cex = 2) plot(x = 1:1465, y = results.NuPoP[,3], type = "n", ylim = c(-0.05, 1), xlab = "Position from the EcoRI site #1", ylab = "probability/occupancy") title("NuPoP: Seven nucleosomes on the Viterbi path") polygon(c(1, 1:1465, 1465), c(0, results.NuPoP[,3], 0), col = 8) points(x = 1:1465, y = results.NuPoP[,4], type = "l", col = 2) points(x = 1:1465, y = results.NuPoP[, 2], type = "h", col = 4) ################################################### ### code chunk number 9: nuCpos-intro.Rnw:256-276 ################################################### 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) ################################################### ### code chunk number 10: nuCpos-intro.Rnw:307-314 ################################################### 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,] ################################################### ### code chunk number 11: nuCpos-intro.Rnw:326-334 ################################################### 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") ################################################### ### code chunk number 12: nuCpos-intro.Rnw:362-366 ################################################### 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") ################################################### ### code chunk number 13: nuCpos-intro.Rnw:382-397 ################################################### TALS <- paste(scan(file = system.file("extdata", "TALS.fasta", package = "nuCpos"), what = character(), skip = 1), sep = "", collapse = "") for(i in 1:23) cat(substr(TALS, start = (i-1)*80+1, stop = (i-1)*80+80), "\n") TTAGGGx29 <- paste(scan(file = system.file("extdata", "TTAGGGx29.fasta", package = "nuCpos"), what = character(), skip = 1), sep = "", collapse = "") for(i in 1:3) cat(substr(TTAGGGx29, start = (i-1)*80+1, stop = (i-1)*80+80), "\n") mut.results <- mutNuCpos(wtseq = TALS, site = 1464, ins = TTAGGGx29, species = "sc", smoothHBA = TRUE, plot.window = 601, ylim.HBA = c(-15, 0), show.occup.window = TRUE, annotation = data.frame(name = "alpha2", color = "purple", left = 1534, right = 1559), full = TRUE) ################################################### ### code chunk number 14: nuCpos-intro.Rnw:431-432 ################################################### mut.results[(((1811+76)*2)-3):(((1811+76)*2)+3),]