## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.width = 6, fig.height = 4 ) ## ----setup-------------------------------------------------------------------- library(idpr) ## ----------------------------------------------------------------------------- #BiocManager::install("idpr") ## ----------------------------------------------------------------------------- #devtools::install_github("wmm27/idpr") ## ----------------------------------------------------------------------------- HUMAN_P53 <- TP53Sequences[2] print(HUMAN_P53) ## ----------------------------------------------------------------------------- P53_msh <- meanScaledHydropathy(HUMAN_P53) print(P53_msh) ## ----------------------------------------------------------------------------- P53_nc <- netCharge(HUMAN_P53, averaged = TRUE) print(P53_nc) ## ----include = FALSE---------------------------------------------------------- P53_msh <- round(P53_msh, 3) P53_nc <- round(P53_nc, 3) ## ----------------------------------------------------------------------------- chargeHydropathyPlot(HUMAN_P53) + ggplot2::annotate("text", x = P53_msh, y = P53_nc + 0.1, #offset from point label = paste("(", P53_msh, ", ", P53_nc, ")", collapse = "", sep = "")) ## ----------------------------------------------------------------------------- TP53_Sequences <- TP53Sequences print(TP53_Sequences) ## ----------------------------------------------------------------------------- gg <- chargeHydropathyPlot( sequence = TP53_Sequences, pKaSet = "IPC_protein") plot(gg) ## ----------------------------------------------------------------------------- chargeHydropathyPlot( sequence = TP53_Sequences, pKaSet = "EMBOSS") #Using EMBOSS pKa set ## ----------------------------------------------------------------------------- foldIndexR(sequence = HUMAN_P53, plotResults = TRUE) ## ----------------------------------------------------------------------------- meanScaledHydropathy(HUMAN_P53) ## ----------------------------------------------------------------------------- P53_shg <- scaledHydropathyGlobal(HUMAN_P53) head(P53_shg) ## ----------------------------------------------------------------------------- scaledHydropathyGlobal(HUMAN_P53, plotResults = TRUE) ## ----------------------------------------------------------------------------- P53_shg <- scaledHydropathyGlobal(HUMAN_P53) sequenceMap(sequence = P53_shg$AA, property = P53_shg$Hydropathy, customColors = c("chocolate1", "grey65", "skyblue3")) ## ----------------------------------------------------------------------------- P53_shl <- scaledHydropathyLocal(HUMAN_P53, plotResults = FALSE) head(P53_shl) ## ----------------------------------------------------------------------------- scaledHydropathyLocal(HUMAN_P53, plotResults = TRUE) ## ----------------------------------------------------------------------------- scaledHydropathyLocal(HUMAN_P53, window = 3, plotResults = TRUE) ## ----------------------------------------------------------------------------- netCharge(HUMAN_P53) ## ----------------------------------------------------------------------------- netCharge(HUMAN_P53, averaged = TRUE) ## ----------------------------------------------------------------------------- netCharge(HUMAN_P53, pH = 5.5) netCharge(HUMAN_P53, pH = 7) netCharge(HUMAN_P53, pH = 8) ## ----------------------------------------------------------------------------- netCharge(HUMAN_P53, pKaSet = "IPC_protein") netCharge(HUMAN_P53, pKaSet = "IPC_peptide") netCharge(HUMAN_P53, pKaSet = "EMBOSS") ## ----include=FALSE------------------------------------------------------------ charged_aa <- c("C", "D", "E", "H", "K", "R", "Y", "NH3", "COO") aa_pKa <- c(8.55, 3.67, 4.25, 6.54, 10.40, 12.3, 9.84, 9.28, 1.99) custom_pKa <- data.frame(AA = charged_aa, pKa = aa_pKa) ## ----------------------------------------------------------------------------- print(custom_pKa) netCharge(HUMAN_P53, pKaSet = custom_pKa, includeTermini = FALSE) ## ----------------------------------------------------------------------------- P53_ccg <- chargeCalculationGlobal(HUMAN_P53) head(P53_ccg) ## ----------------------------------------------------------------------------- chargeCalculationGlobal(HUMAN_P53, plotResults = TRUE) ## ----------------------------------------------------------------------------- P53_ccg <- chargeCalculationGlobal(HUMAN_P53) #repeating from above sequenceMap(sequence = P53_ccg$AA, property = P53_ccg$Charge, customColors = c("red", "blue", "grey65")) ## ----------------------------------------------------------------------------- P53_ccg <- chargeCalculationGlobal(HUMAN_P53, sumTermini = FALSE) head(P53_ccg) ## ----------------------------------------------------------------------------- P53_ccg <- chargeCalculationGlobal(HUMAN_P53, includeTermini = FALSE) head(P53_ccg) ## ----------------------------------------------------------------------------- P53_cgl <- chargeCalculationLocal(HUMAN_P53) head(P53_cgl) ## ----------------------------------------------------------------------------- chargeCalculationLocal(HUMAN_P53, plotResults = TRUE) ## ----------------------------------------------------------------------------- chargeCalculationLocal(HUMAN_P53, window = 11, plotResults = TRUE) ## ----------------------------------------------------------------------------- citation("ggplot2") ## ----------------------------------------------------------------------------- R.version.string ## ----------------------------------------------------------------------------- as.data.frame(Sys.info()) ## ----------------------------------------------------------------------------- sessionInfo() ## ----results="asis"----------------------------------------------------------- citation()