GCAT5.0 released
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Minh
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# R CMD INSTALL "C:/My Documents/GLBRC Projects/10_HTS_1/package/test.package"
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library(test.package)
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USDA1.controls =c(paste("A0",1:9,sep=""), paste("A",10:12,sep=""),
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paste("H0",1:9,sep=""), paste("H",10:12,sep=""),
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"E10", "E11", "F08", "F09", "G08", "G09", "P.7",
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paste(LETTERS[2:7],"01",sep=""), paste(LETTERS[2:7],"12",sep=""))
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Lalle1.controls = c("A11", "H11", paste(LETTERS[1:8],"01",sep=""),
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paste(LETTERS[1:8],"12",sep=""), "A02")
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path = "C:/My Documents/GLBRC Projects/10_HTS_1/data"
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# Analyze the Lalle1 Plate
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file = "Lalle1_media1_rep1_082909.csv"
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data = load.data(, path, file, column.names = c("Plate.ID", "Well", "OD", "Time"),
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time.format = "%Y-%m-%d %H:%M:%S")
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Lalle1 = analyze.screen(data, well.numbers = 1:768, scale = 0.5, remove.points = 1:2,
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controls = Lalle1.controls , save.jpegs = F, autopilot = T)
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write.csv(Lalle1, file = "Lalle1_analysis.csv")
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# Step by step
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analyze.screen(data, scale = 0.5, remove.points = 1:2,
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controls = Lalle1.controls , save.jpegs = F, autopilot = F)
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#Analyze the USDA1 Plate
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file = "USDA1_Media1_Rep1_061909.csv"
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data2 = load.data(, path, file, column.names = c("Plate.ID", "Well", "OD", "Time"),
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time.format = "%Y-%m-%d %H:%M:%S")
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USDA1 = analyze.screen(data2, scale = 0.5, remove.points = 1:2,
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controls = Lalle1.controls , save.jpegs = F, autopilot = T)
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write.csv(USDA1, file = "USDA1_analysis.csv")
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best.wells(Lalle1, "3.1")
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#Setup
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# Load from WIP files
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setwd( )
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source("GLBRC Projects/10_HTS_1/package/test.package/R/load.R")
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source("GLBRC Projects/10_HTS_1/package/test.package/R/misc_functions.R")
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source("GLBRC Projects/10_HTS_1/package/test.package/R/curve.shapes.R")
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source("GLBRC Projects/10_HTS_1/package/test.package/R/logistic.response.new.R")
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source("GLBRC Projects/10_HTS_1/package/test.package/R/analyze.main.R")
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source("GLBRC Projects/10_HTS_1/package/test.package/R/main.R")
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source("GLBRC Projects/10_HTS_1/package/test.package/R/top.wells.R")
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# OR:
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# R CMD INSTALL "C:/My Documents/GLBRC Projects/10_HTS_1/package/test.package"
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library(test.package)
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?analyze.screen
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?load.data
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?test.package
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?top.wells
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?analyze.main
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path = "C:/My Documents/GLBRC Projects/10_HTS_1/data"
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file = "072209a_USDA_screen.csv"
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controls= c(paste(LETTERS[1:8],"01",sep=""),paste(LETTERS[1:8],"12",sep=""))
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data1 = load.data(, path, file, column.names = c("Plate.ID", "Well", "OD", "Time"),
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time.format = "%Y-%m-%d %H:%M:%S")
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output = analyze.screen(data1, scale = 0.5, controls = controls, save.jpegs = F, autopilot = T)
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# Step by step:
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analyze.screen(data1, scale = 0.5, controls = controls, save.jpegs = F, autopilot = F)
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# equivalent (Save JPEGS):
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analyze.screen(, path, file, controls = controls, save.jpegs = T, autopilot = F)
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# Load another set
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file = "YeastScreenData_ValidationRun_rawdata_4-16-09.csv"
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controls=c("A11", "H11", paste(LETTERS[1:8],"01",sep=""), paste(LETTERS[1:8],"12",sep=""))
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data2 = load.data(, path, file, column.names = c("Plate.name", "Well", "OD600", "Timestamp"),
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time.format = "%m/%d/%Y %H:%M:%S")
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output2 = analyze.screen(data2, scale = 0.5, remove.points = 1, controls = controls, save.jpegs = F, autopilot = T)
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# Step by step:
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analyze.screen(data2, well.numbers = 584, scale = 0.5, controls = controls, remove.points = 1, save.jpegs = F, autopilot = F)
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# equivalent (save JPEGS):
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analyze.screen(, path, file, controls = controls, remove.points = 1:2, save.jpegs = T, autopilot = F)
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output2[is.in.character("Error", output2[,4]),1] -> e
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output2[is.in.character("above", output2[,4]),1] -> ab
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best.wells(output3)
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# Load a single plate set
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file = "YeastGrowthUSDAYPD30degrees3-19-09.csv"
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controls=c(paste("A0",1:9,sep=""), paste("A",10:12,sep=""),
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paste("H0",1:9,sep=""), paste("H",10:12,sep=""),
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"E10", "E11", "F08", "F09", "G08", "G09", "P.7",
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paste(LETTERS[2:7],"01",sep=""), paste(LETTERS[2:7],"12",sep=""))
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data3 = load.data(, path, file, single.plate = T, single.columns = c("Time", "A1", "H12"), time.format = "%S")
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output3 = analyze.screen(data3, scale = 0.5, remove.points = 1:2, controls = controls, save.jpegs = F, autopilot = T)
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# Step by step:
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analyze.screen(data3, scale = 0.5, controls = controls, remove.points = 1:2, save.jpegs = F, autopilot = F)
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# equivalent (save JPEGS):
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analyze.screen(, path, file, controls = controls, remove.points = 1:2, save.jpegs = T, autopilot = F)
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output = analyze.main(data1, scale = 0.5, controls = control.wells, remove.outliers = TRUE, autopilot = TRUE)
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output2 = analyze.main(data1, controls = control.wells, remove.outliers = TRUE, autopilot = FALSE)
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summary(output2)
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output[is.finite(output$c) & output$c<0, ]$well.number
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output[is.finite(output$growth.ratio),]$well.number
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out.good.fit = output[output$curve.type == "" | output$curve.type == ": TANKING",]
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summary(out.good.fit)
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out.good.fit[,desired.columns]
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out.lin.fit = output[(output$linear.fit) & (output$curve.type == "" | output$curve.type == ": TANKING"),]
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summary(out.lin.fit)
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out.lin.fit[,desired.columns]
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out.lin.fit = output[(output$linear.fit & output$logistic.fit ) & (output$curve.type == "" | output$curve.type == ": TANKING"),]
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out.lin.fit$well.number
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out.lin.fit[,desired.columns]
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out.log.fit = output[(output$action == "Logistic model only.") & (output$curve.type == "" | output$curve.type == ": TANKING"),]
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summary(out.log.fit)
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out.log.fit[,desired.columns]
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out.no.s = output[output$curve.type == ": NOT S-SHAPE",]
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summary(out.no.s[,desired.columns])
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attention = output[grepl("(!)", output$remarks) & !output$curve.type == ": TANKING" ,]
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summary(attention[,desired.columns])
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out.no.fit = output[!(output$logistic.fit | output$linear.fit) & (output$curve.type == "" | output$curve.type == ": TANKING"),]
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summary(out.no.fit[,desired.columns])
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compare(output[output$total.growth <0,]$well.number)
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analyze.main(data1, well.numbers = out.no.s$well.number, controls = control.wells, remove.outliers = T, autopilot = FALSE)
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analyze.main(data1, well.numbers = attention$well.number, controls = control.wells, remove.outliers = T, autopilot = FALSE)
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results[results$Plate.name == "041609a.GLBRC2000P.1" & results$Well == "G06",]
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